plink: plink.xml comparison

comparison plink.xml @ 3:4c3690a9d729 draft default tip

Fix help text formatting

author	blankenberg
date	Tue, 19 Nov 2019 21:35:42 +0000
parents	ed946e888494
children

comparison

equal deleted inserted replaced

-:ed946e888494
+:4c3690a9d729
 <data name="OUTPUT_plink_var_ranges" format="plink.var.ranges" label="${tool.name} on ${on_string}: plink.var.ranges" from_work_dir="plink.var.ranges" hidden="True"/>
 <data name="OUTPUT_plink_vcf" format="vcf" label="${tool.name} on ${on_string}: plink.vcf" from_work_dir="plink.vcf" hidden="True"/>
 <data name="OUTPUT_plink_log" format="plink.log" label="${tool.name} on ${on_string}: plink.log" from_work_dir="plink.log" hidden="False"/>
 </outputs>
 <help><![CDATA[
+::
-PLINK v1.90b4 64-bit (20 Mar 2017)             www.cog-genomics.org/plink/1.9/
-(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3
+PLINK v1.90b4 64-bit (20 Mar 2017)             www.cog-genomics.org/plink/1.9/
-In the command line flag definitions that follow,
+(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3
-* [square brackets] denote a required parameter, where the text between the
-brackets describes its nature.
+In the command line flag definitions that follow,
-* <angle brackets> denote an optional modifier (or if '|' is present, a set
+* [square brackets] denote a required parameter, where the text between the
-of mutually exclusive optional modifiers).  Use the EXACT text in the
+brackets describes its nature.
-definition, e.g. '--dummy acgt'.
+* <angle brackets> denote an optional modifier (or if '|' is present, a set
-* There's one exception to the angle brackets/exact text rule: when an angle
+of mutually exclusive optional modifiers).  Use the EXACT text in the
-bracket term ends with '=[value]', '[value]' designates a variable
+definition, e.g. '--dummy acgt'.
-parameter.
+* There's one exception to the angle brackets/exact text rule: when an angle
-* {curly braces} denote an optional parameter, where the text between the
+bracket term ends with '=[value]', '[value]' designates a variable
-braces describes its nature.
+parameter.
-* An ellipsis (...) indicates that you may enter multiple parameters of the
+* {curly braces} denote an optional parameter, where the text between the
-specified type.
+braces describes its nature.
+* An ellipsis (...) indicates that you may enter multiple parameters of the
-plink [input flag(s)...] {command flag(s)...} {other flag(s)...}
+specified type.
-plink --help {flag name(s)...}
+plink [input flag(s)...] {command flag(s)...} {other flag(s)...}
-Most PLINK runs require exactly one main input fileset.  The following flags
+plink --help {flag name(s)...}
-are available for defining its form and location:
+Most PLINK runs require exactly one main input fileset.  The following flags
---bfile {prefix} : Specify .bed + .bim + .fam prefix (default 'plink').
+are available for defining its form and location:
---bed [filename] : Specify full name of .bed file.
---bim [filename] : Specify full name of .bim file.
+--bfile {prefix} : Specify .bed + .bim + .fam prefix (default 'plink').
---fam [filename] : Specify full name of .fam file.
+--bed [filename] : Specify full name of .bed file.
+--bim [filename] : Specify full name of .bim file.
---keep-autoconv  : With --file/--tfile/--lfile/--vcf/--bcf/--data/--23file,
+--fam [filename] : Specify full name of .fam file.
-don't delete autogenerated binary fileset at end of run.
+--keep-autoconv  : With --file/--tfile/--lfile/--vcf/--bcf/--data/--23file,
---file {prefix}  : Specify .ped + .map filename prefix (default 'plink').
+don't delete autogenerated binary fileset at end of run.
---ped [filename] : Specify full name of .ped file.
---map [filename] : Specify full name of .map file.
+--file {prefix}  : Specify .ped + .map filename prefix (default 'plink').
+--ped [filename] : Specify full name of .ped file.
---no-fid         : .fam/.ped file does not contain column 1 (family ID).
+--map [filename] : Specify full name of .map file.
---no-parents     : .fam/.ped file does not contain columns 3-4 (parents).
---no-sex         : .fam/.ped file does not contain column 5 (sex).
+--no-fid         : .fam/.ped file does not contain column 1 (family ID).
---no-pheno       : .fam/.ped file does not contain column 6 (phenotype).
+--no-parents     : .fam/.ped file does not contain columns 3-4 (parents).
+--no-sex         : .fam/.ped file does not contain column 5 (sex).
---tfile {prefix} : Specify .tped + .tfam filename prefix (default 'plink').
+--no-pheno       : .fam/.ped file does not contain column 6 (phenotype).
---tped [fname]   : Specify full name of .tped file.
---tfam [fname]   : Specify full name of .tfam file.
+--tfile {prefix} : Specify .tped + .tfam filename prefix (default 'plink').
+--tped [fname]   : Specify full name of .tped file.
---lfile {prefix} : Specify .lgen + .map + .fam (long-format fileset) prefix.
+--tfam [fname]   : Specify full name of .tfam file.
---lgen [fname]   : Specify full name of .lgen file.
---reference [fn] : Specify default allele file accompanying .lgen input.
+--lfile {prefix} : Specify .lgen + .map + .fam (long-format fileset) prefix.
---allele-count   : When used with --lfile/--lgen + --reference, specifies
+--lgen [fname]   : Specify full name of .lgen file.
-that the .lgen file contains reference allele counts.
+--reference [fn] : Specify default allele file accompanying .lgen input.
+--allele-count   : When used with --lfile/--lgen + --reference, specifies
---vcf [filename] : Specify full name of .vcf or .vcf.gz file.
+that the .lgen file contains reference allele counts.
---bcf [filename] : Specify full name of BCF2 file.
+--vcf [filename] : Specify full name of .vcf or .vcf.gz file.
---data {prefix}  : Specify Oxford .gen + .sample prefix (default 'plink').
+--bcf [filename] : Specify full name of BCF2 file.
---gen [filename] : Specify full name of .gen or .gen.gz file.
---bgen [f] <snpid-chr> : Specify full name of .bgen file.
+--data {prefix}  : Specify Oxford .gen + .sample prefix (default 'plink').
---sample [fname] : Specify full name of .sample file.
+--gen [filename] : Specify full name of .gen or .gen.gz file.
+--bgen [f] <snpid-chr> : Specify full name of .bgen file.
---23file [fname] {FID} {IID} {sex} {pheno} {pat. ID} {mat. ID} :
+--sample [fname] : Specify full name of .sample file.
-Specify 23andMe input file.
+--23file [fname] {FID} {IID} {sex} {pheno} {pat. ID} {mat. ID} :
---grm-gz {prfx}  : Specify .grm.gz + .grm.id (GCTA rel. matrix) prefix.
+Specify 23andMe input file.
---grm-bin {prfx} : Specify .grm.bin + .grm.N.bin + .grm.id (GCTA triangular
-binary relationship matrix) filename prefix.
+--grm-gz {prfx}  : Specify .grm.gz + .grm.id (GCTA rel. matrix) prefix.
+--grm-bin {prfx} : Specify .grm.bin + .grm.N.bin + .grm.id (GCTA triangular
---dummy [sample ct] [SNP ct] {missing geno freq} {missing pheno freq}
+binary relationship matrix) filename prefix.
-<acgt | 1234 | 12> <scalar-pheno>
-This generates a fake input dataset with the specified number of samples
+--dummy [sample ct] [SNP ct] {missing geno freq} {missing pheno freq}
-and SNPs.  By default, the missing genotype and phenotype frequencies are
+<acgt | 1234 | 12> <scalar-pheno>
-zero, and genotypes are As and Bs (change the latter with
+This generates a fake input dataset with the specified number of samples
-'acgt'/'1234'/'12').  The 'scalar-pheno' modifier causes a normally
+and SNPs.  By default, the missing genotype and phenotype frequencies are
-distributed scalar phenotype to be generated instead of a binary one.
+zero, and genotypes are As and Bs (change the latter with
+'acgt'/'1234'/'12').  The 'scalar-pheno' modifier causes a normally
---simulate [simulation parameter file] <tags | haps> <acgt | 1234 | 12>
+distributed scalar phenotype to be generated instead of a binary one.
---simulate-qt [simulation parameter file] <tags | haps> <acgt | 1234 | 12>
---simulate generates a fake input dataset with disease-associated SNPs,
+--simulate [simulation parameter file] <tags | haps> <acgt | 1234 | 12>
-while --simulate-qt generates a dataset with quantitative trait loci.
+--simulate-qt [simulation parameter file] <tags | haps> <acgt | 1234 | 12>
+--simulate generates a fake input dataset with disease-associated SNPs,
-Output files have names of the form 'plink.{extension}' by default.  You can
+while --simulate-qt generates a dataset with quantitative trait loci.
-change the 'plink' prefix with
+Output files have names of the form 'plink.{extension}' by default.  You can
---out [prefix]   : Specify prefix for output files.
+change the 'plink' prefix with
-Most runs also require at least one of the following commands:
+--out [prefix]   : Specify prefix for output files.
---make-bed
+Most runs also require at least one of the following commands:
-Create a new binary fileset.  Unlike the automatic text-to-binary
-converters (which only heed chromosome filters), this supports all of
+--make-bed
-PLINK's filtering flags.
+Create a new binary fileset.  Unlike the automatic text-to-binary
---make-just-bim
+converters (which only heed chromosome filters), this supports all of
---make-just-fam
+PLINK's filtering flags.
-Variants of --make-bed which only write a new .bim or .fam file.  Can be
+--make-just-bim
-used with only .bim/.fam input.
+--make-just-fam
-USE THESE CAUTIOUSLY.  It is very easy to desynchronize your binary
+Variants of --make-bed which only write a new .bim or .fam file.  Can be
-genotype data and your .bim/.fam indexes if you use these commands
+used with only .bim/.fam input.
-improperly.  If you have any doubt, stick with --make-bed.
+USE THESE CAUTIOUSLY.  It is very easy to desynchronize your binary
+genotype data and your .bim/.fam indexes if you use these commands
---recode [output format] <01 | 12> <tab | tabx | spacex | bgz | gen-gz>
+improperly.  If you have any doubt, stick with --make-bed.
-<include-alt> <omit-nonmale-y>
-Create a new text fileset with all filters applied.  The following output
+--recode [output format] <01 | 12> <tab | tabx | spacex | bgz | gen-gz>
-formats are supported:
+<include-alt> <omit-nonmale-y>
-* '23': 23andMe 4-column format.  This can only be used on a single
+Create a new text fileset with all filters applied.  The following output
-sample's data (--keep may be handy), and does not support multicharacter
+formats are supported:
-allele codes.
+* '23': 23andMe 4-column format.  This can only be used on a single
-* 'A': Sample-major additive (0/1/2) coding, suitable for loading from R.
+sample's data (--keep may be handy), and does not support multicharacter
-If you need uncounted alleles to be named in the header line, add the
+allele codes.
-'include-alt' modifier.
+* 'A': Sample-major additive (0/1/2) coding, suitable for loading from R.
-* 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding.
+If you need uncounted alleles to be named in the header line, add the
-Also supports 'include-alt'.
+'include-alt' modifier.
-* 'A-transpose': Variant-major 0/1/2.
+* 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding.
-* 'beagle': Unphased per-autosome .dat and .map files, readable by early
+Also supports 'include-alt'.
-BEAGLE versions.
+* 'A-transpose': Variant-major 0/1/2.
-* 'beagle-nomap': Single .beagle.dat file.
+* 'beagle': Unphased per-autosome .dat and .map files, readable by early
-* 'bimbam': Regular BIMBAM format.
+BEAGLE versions.
-* 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file.  Does not
+* 'beagle-nomap': Single .beagle.dat file.
-support multiple chromosomes.
+* 'bimbam': Regular BIMBAM format.
-* 'fastphase': Per-chromosome fastPHASE files, with
+* 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file.  Does not
-.chr-[chr #].recode.phase.inp filename extensions.
+support multiple chromosomes.
-* 'fastphase-1chr': Single .recode.phase.inp file.  Does not support
+* 'fastphase': Per-chromosome fastPHASE files, with
-multiple chromosomes.
+.chr-[chr #].recode.phase.inp filename extensions.
-* 'HV': Per-chromosome Haploview files, with .chr-[chr #][.ped + .info]
+* 'fastphase-1chr': Single .recode.phase.inp file.  Does not support
-filename extensions.
+multiple chromosomes.
-* 'HV-1chr': Single Haploview .ped + .info file pair.  Does not support
+* 'HV': Per-chromosome Haploview files, with .chr-[chr #][.ped + .info]
-multiple chromosomes.
+filename extensions.
-* 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile.
+* 'HV-1chr': Single Haploview .ped + .info file pair.  Does not support
-* 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile +
+multiple chromosomes.
---reference.
+* 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile.
-* 'list': Single genotype-based list, up to 4 lines per variant.  To omit
+* 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile +
-nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y' modifier.
+--reference.
-* 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a
+* 'list': Single genotype-based list, up to 4 lines per variant.  To omit
-genotype-based list which omits the most common genotype for each
+nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y' modifier.
-variant.  Also supports 'omit-nonmale-y'.
+* 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a
-* 'oxford': Oxford-format .gen + .sample.  With the 'gen-gz' modifier, the
+genotype-based list which omits the most common genotype for each
-.gen file is gzipped.
+variant.  Also supports 'omit-nonmale-y'.
-* 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file.
+* 'oxford': Oxford-format .gen + .sample.  With the 'gen-gz' modifier, the
-* 'compound-genotypes': Same as 'ped', except that the space between each
+.gen file is gzipped.
-pair of same-variant allele codes is removed.
+* 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file.
-* 'structure': Structure-format.
+* 'compound-genotypes': Same as 'ped', except that the space between each
-* 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with
+pair of same-variant allele codes is removed.
---tfile.
+* 'structure': Structure-format.
-* 'vcf', 'vcf-fid', 'vcf-iid': VCFv4.2.  'vcf-fid' and 'vcf-iid' cause
+* 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with
-family IDs or within-family IDs respectively to be used for the sample
+--tfile.
-IDs in the last header row, while 'vcf' merges both IDs and puts an
+* 'vcf', 'vcf-fid', 'vcf-iid': VCFv4.2.  'vcf-fid' and 'vcf-iid' cause
-underscore between them.  If the 'bgz' modifier is added, the VCF file is
+family IDs or within-family IDs respectively to be used for the sample
-block-gzipped.
+IDs in the last header row, while 'vcf' merges both IDs and puts an
-The A2 allele is saved as the reference and normally flagged as not based
+underscore between them.  If the 'bgz' modifier is added, the VCF file is
-on a real reference genome (INFO:PR).  When it is important for reference
+block-gzipped.
-alleles to be correct, you'll also want to include --a2-allele and
+The A2 allele is saved as the reference and normally flagged as not based
---real-ref-alleles in your command.
+on a real reference genome (INFO:PR).  When it is important for reference
-In addition,
+alleles to be correct, you'll also want to include --a2-allele and
-* The '12' modifier causes A1 (usually minor) alleles to be coded as '1'
+--real-ref-alleles in your command.
-and A2 alleles to be coded as '2', while '01' maps A1 -> 0 and A2 -> 1.
+In addition,
-* The 'tab' modifier makes the output mostly tab-delimited instead of
+* The '12' modifier causes A1 (usually minor) alleles to be coded as '1'
-mostly space-delimited.  'tabx' and 'spacex' force all tabs and all
+and A2 alleles to be coded as '2', while '01' maps A1 -> 0 and A2 -> 1.
-spaces, respectively.
+* The 'tab' modifier makes the output mostly tab-delimited instead of
+mostly space-delimited.  'tabx' and 'spacex' force all tabs and all
---flip-scan <verbose>
+spaces, respectively.
-(alias: --flipscan)
-LD-based scan for case/control strand inconsistency.
+--flip-scan <verbose>
+(alias: --flipscan)
---write-covar
+LD-based scan for case/control strand inconsistency.
-If a --covar file is loaded, --make-bed/--make-just-fam and --recode
-automatically generate an updated version (with all filters applied).
+--write-covar
-However, if you do not wish to simultaneously generate a new genotype file,
+If a --covar file is loaded, --make-bed/--make-just-fam and --recode
-you can use --write-covar to just produce a pruned covariate file.
+automatically generate an updated version (with all filters applied).
+However, if you do not wish to simultaneously generate a new genotype file,
---write-cluster <omit-unassigned>
+you can use --write-covar to just produce a pruned covariate file.
-If clusters are specified with --within/--family, this generates a new
-cluster file (with all filters applied).  The 'omit-unassigned' modifier
+--write-cluster <omit-unassigned>
-causes unclustered samples to be omitted from the file; otherwise their
+If clusters are specified with --within/--family, this generates a new
-cluster is 'NA'.
+cluster file (with all filters applied).  The 'omit-unassigned' modifier
+causes unclustered samples to be omitted from the file; otherwise their
---write-set
+cluster is 'NA'.
---set-table
-If sets have been defined, --write-set dumps 'END'-terminated set
+--write-set
-membership lists to {output prefix}.set, while --set-table writes a
+--set-table
-variant-by-set membership table to {output prefix}.set.table.
+If sets have been defined, --write-set dumps 'END'-terminated set
+membership lists to {output prefix}.set, while --set-table writes a
---merge [.ped filename] [.map filename]
+variant-by-set membership table to {output prefix}.set.table.
---merge [text fileset prefix]
---bmerge [.bed filename] [.bim filename] [.fam filename]
+--merge [.ped filename] [.map filename]
---bmerge [binary fileset prefix]
+--merge [text fileset prefix]
-Merge the given fileset with the initially loaded fileset, writing the
+--bmerge [.bed filename] [.bim filename] [.fam filename]
-result to {output prefix}.bed + .bim + .fam.  (It is no longer necessary to
+--bmerge [binary fileset prefix]
-simultaneously specify --make-bed.)
+Merge the given fileset with the initially loaded fileset, writing the
---merge-list [filename]
+result to {output prefix}.bed + .bim + .fam.  (It is no longer necessary to
-Merge all filesets named in the text file with the reference fileset, if
+simultaneously specify --make-bed.)
-one was specified.  (However, this can also be used *without* a reference;
+--merge-list [filename]
-in that case, the newly created fileset is then treated as the reference by
+Merge all filesets named in the text file with the reference fileset, if
-most other PLINK operations.)  The text file is interpreted as follows:
+one was specified.  (However, this can also be used *without* a reference;
-* If a line contains only one name, it is assumed to be the prefix for a
+in that case, the newly created fileset is then treated as the reference by
-binary fileset.
+most other PLINK operations.)  The text file is interpreted as follows:
-* If a line contains exactly two names, they are assumed to be the full
+* If a line contains only one name, it is assumed to be the prefix for a
-filenames for a text fileset (.ped first, then .map).
+binary fileset.
-* If a line contains exactly three names, they are assumed to be the full
+* If a line contains exactly two names, they are assumed to be the full
-filenames for a binary fileset (.bed, then .bim, then .fam).
+filenames for a text fileset (.ped first, then .map).
+* If a line contains exactly three names, they are assumed to be the full
---write-snplist
+filenames for a binary fileset (.bed, then .bim, then .fam).
---list-23-indels
---write-snplist writes a .snplist file listing the names of all variants
+--write-snplist
-which pass the filters and inclusion thresholds you've specified, while
+--list-23-indels
---list-23-indels writes the subset with 23andMe-style indel calls (D/I
+--write-snplist writes a .snplist file listing the names of all variants
-allele codes).
+which pass the filters and inclusion thresholds you've specified, while
+--list-23-indels writes the subset with 23andMe-style indel calls (D/I
---list-duplicate-vars <require-same-ref> <ids-only> <suppress-first>
+allele codes).
---list-duplicate-vars writes a .dupvar file describing all groups of
-variants with matching positions and allele codes.
+--list-duplicate-vars <require-same-ref> <ids-only> <suppress-first>
-* By default, A1/A2 allele assignments are ignored; use 'require-same-ref'
+--list-duplicate-vars writes a .dupvar file describing all groups of
-to override this.
+variants with matching positions and allele codes.
-* Normally, the report contains position and allele codes.  To remove them
+* By default, A1/A2 allele assignments are ignored; use 'require-same-ref'
-(and produce a file directly usable with e.g. --extract/--exclude), use
+to override this.
-'ids-only'.  Note that this command will fail in 'ids-only' mode if any
+* Normally, the report contains position and allele codes.  To remove them
-of the reported IDs are not unique.
+(and produce a file directly usable with e.g. --extract/--exclude), use
-* 'suppress-first' causes the first variant ID in each group to be omitted
+'ids-only'.  Note that this command will fail in 'ids-only' mode if any
-from the report.
+of the reported IDs are not unique.
+* 'suppress-first' causes the first variant ID in each group to be omitted
---freq <counts | case-control> <gz>
+from the report.
---freqx <gz>
---freq generates a basic allele frequency (or count, if the 'counts'
+--freq <counts | case-control> <gz>
-modifier is present) report.  This can be combined with --within/--family
+--freqx <gz>
-to produce a cluster-stratified allele frequency/count report instead, or
+--freq generates a basic allele frequency (or count, if the 'counts'
-the 'case-control' modifier to report case and control allele frequencies
+modifier is present) report.  This can be combined with --within/--family
-separately.
+to produce a cluster-stratified allele frequency/count report instead, or
---freqx generates a more detailed genotype count report, designed for use
+the 'case-control' modifier to report case and control allele frequencies
-with --read-freq.
+separately.
+--freqx generates a more detailed genotype count report, designed for use
---missing <gz>
+with --read-freq.
-Generate sample- and variant-based missing data reports.  If clusters are
-defined, the variant-based report is cluster-stratified.  'gz' causes the
+--missing <gz>
-output files to be gzipped.
+Generate sample- and variant-based missing data reports.  If clusters are
+defined, the variant-based report is cluster-stratified.  'gz' causes the
---test-mishap
+output files to be gzipped.
-Check for association between missing calls and flanking haplotypes.
+--test-mishap
---hardy <midp> <gz>
+Check for association between missing calls and flanking haplotypes.
-Generate a Hardy-Weinberg exact test p-value report.  (This does NOT
-simultaneously filter on the p-value any more; use --hwe for that.)  With
+--hardy <midp> <gz>
-the 'midp' modifier, the test applies the mid-p adjustment described in
+Generate a Hardy-Weinberg exact test p-value report.  (This does NOT
-Graffelman J, Moreno V (2013) The mid p-value in exact tests for
+simultaneously filter on the p-value any more; use --hwe for that.)  With
-Hardy-Weinberg Equilibrium.
+the 'midp' modifier, the test applies the mid-p adjustment described in
+Graffelman J, Moreno V (2013) The mid p-value in exact tests for
---mendel <summaries-only>
+Hardy-Weinberg Equilibrium.
-Generate a Mendel error report.  The 'summaries-only' modifier causes the
-.mendel file (listing every single error) to be skipped.
+--mendel <summaries-only>
+Generate a Mendel error report.  The 'summaries-only' modifier causes the
---het <small-sample> <gz>
+.mendel file (listing every single error) to be skipped.
---ibc
-Estimate inbreeding coefficients.  --het reports method-of-moments
+--het <small-sample> <gz>
-estimates, while --ibc calculates all three values described in Yang J, Lee
+--ibc
-SH, Goddard ME and Visscher PM (2011) GCTA: A Tool for Genome-wide Complex
+Estimate inbreeding coefficients.  --het reports method-of-moments
-Trait Analysis.  (That paper also describes the relationship matrix
+estimates, while --ibc calculates all three values described in Yang J, Lee
-computation we reimplement.)
+SH, Goddard ME and Visscher PM (2011) GCTA: A Tool for Genome-wide Complex
-* These functions require decent MAF estimates.  If there are very few
+Trait Analysis.  (That paper also describes the relationship matrix
-samples in your immediate fileset, --read-freq is practically mandatory
+computation we reimplement.)
-since imputed MAFs are wildly inaccurate in that case.
+* These functions require decent MAF estimates.  If there are very few
-* They also assume the marker set is in approximate linkage equilibrium.
+samples in your immediate fileset, --read-freq is practically mandatory
-* By default, --het omits the n/(n-1) multiplier in Nei's expected
+since imputed MAFs are wildly inaccurate in that case.
-homozygosity formula.  The 'small-sample' modifier causes it to be
+* They also assume the marker set is in approximate linkage equilibrium.
-included, while forcing --het to use MAFs imputed from founders in the
+* By default, --het omits the n/(n-1) multiplier in Nei's expected
-immediate dataset.
+homozygosity formula.  The 'small-sample' modifier causes it to be
+included, while forcing --het to use MAFs imputed from founders in the
---check-sex {female max F} {male min F}
+immediate dataset.
---check-sex ycount {female max F} {male min F} {female max Y obs}
-{male min Y obs}
+--check-sex {female max F} {male min F}
---check-sex y-only {female max Y obs} {male min Y obs}
+--check-sex ycount {female max F} {male min F} {female max Y obs}
---impute-sex {female max F} {male min F}
+{male min Y obs}
---impute-sex ycount {female max F} {male min F} {female max Y obs}
+--check-sex y-only {female max Y obs} {male min Y obs}
-{male min Y obs}
+--impute-sex {female max F} {male min F}
---impute-sex y-only {female max Y obs} {male min Y obs}
+--impute-sex ycount {female max F} {male min F} {female max Y obs}
---check-sex normally compares sex assignments in the input dataset with
+{male min Y obs}
-those imputed from X chromosome inbreeding coefficients.
+--impute-sex y-only {female max Y obs} {male min Y obs}
-* Make sure that the X chromosome pseudo-autosomal region has been split
+--check-sex normally compares sex assignments in the input dataset with
-off (with e.g. --split-x) before using this.
+those imputed from X chromosome inbreeding coefficients.
-* You also need decent MAF estimates (so, with very few samples in your
+* Make sure that the X chromosome pseudo-autosomal region has been split
-immediate fileset, use --read-freq), and your marker set should be in
+off (with e.g. --split-x) before using this.
-approximate linkage equilibrium.
+* You also need decent MAF estimates (so, with very few samples in your
-* By default, F estimates smaller than 0.2 yield female calls, and values
+immediate fileset, use --read-freq), and your marker set should be in
-larger than 0.8 yield male calls.  If you pass numeric parameter(s) to
+approximate linkage equilibrium.
---check-sex, the first two control these thresholds.
+* By default, F estimates smaller than 0.2 yield female calls, and values
-There are now two modes which consider Y chromosome data.
+larger than 0.8 yield male calls.  If you pass numeric parameter(s) to
-* In 'ycount' mode, gender is still imputed from the X chromosome, but
+--check-sex, the first two control these thresholds.
-female calls are downgraded to ambiguous whenever more than 0 nonmissing
+There are now two modes which consider Y chromosome data.
-Y genotypes are present, and male calls are downgraded when fewer than 0
+* In 'ycount' mode, gender is still imputed from the X chromosome, but
-are present.  (Note that these are counts, not rates.)  These thresholds
+female calls are downgraded to ambiguous whenever more than 0 nonmissing
-are controllable with --check-sex ycount's optional 3rd and 4th numeric
+Y genotypes are present, and male calls are downgraded when fewer than 0
-parameters.
+are present.  (Note that these are counts, not rates.)  These thresholds
-* In 'y-only' mode, gender is imputed from nonmissing Y genotype counts.
+are controllable with --check-sex ycount's optional 3rd and 4th numeric
-The male minimum threshold defaults to 1 instead of zero in this case.
+parameters.
---impute-sex changes sex assignments to the imputed values, and is
+* In 'y-only' mode, gender is imputed from nonmissing Y genotype counts.
-otherwise identical to --check-sex.  It must be used with
+The male minimum threshold defaults to 1 instead of zero in this case.
---make-bed/--recode/--write-covar.
+--impute-sex changes sex assignments to the imputed values, and is
+otherwise identical to --check-sex.  It must be used with
---fst <case-control>
+--make-bed/--recode/--write-covar.
-(alias: --Fst)
-Estimate Wright's Fst for each autosomal diploid variant using the method
+--fst <case-control>
-introduced in Weir BS, Cockerham CC (1984) Estimating F-statistics for the
+(alias: --Fst)
-analysis of population structure, given a set of subpopulations defined via
+Estimate Wright's Fst for each autosomal diploid variant using the method
---within.  Raw and weighted global means are also reported.
+introduced in Weir BS, Cockerham CC (1984) Estimating F-statistics for the
-* If you're interested in the global means, it is usually best to perform
+analysis of population structure, given a set of subpopulations defined via
-this calculation on a marker set in approximate linkage equilibrium.
+--within.  Raw and weighted global means are also reported.
-* If you have only two subpopulations, you can represent them with
+* If you're interested in the global means, it is usually best to perform
-case/control status and use the 'case-control' modifier.
+this calculation on a marker set in approximate linkage equilibrium.
+* If you have only two subpopulations, you can represent them with
---indep [window size]<kb> [step size (variant ct)] [VIF threshold]
+case/control status and use the 'case-control' modifier.
---indep-pairwise [window size]<kb> [step size (variant ct)] [r^2 threshold]
---indep-pairphase [window size]<kb> [step size (variant ct)] [r^2 threshold]
+--indep [window size]<kb> [step size (variant ct)] [VIF threshold]
-Generate a list of markers in approximate linkage equilibrium.  With the
+--indep-pairwise [window size]<kb> [step size (variant ct)] [r^2 threshold]
-'kb' modifier, the window size is in kilobase instead of variant count
+--indep-pairphase [window size]<kb> [step size (variant ct)] [r^2 threshold]
-units.  (Pre-'kb' space is optional, i.e. '--indep-pairwise 500 kb 5 0.5'
+Generate a list of markers in approximate linkage equilibrium.  With the
-and '--indep-pairwise 500kb 5 0.5' have the same effect.)
+'kb' modifier, the window size is in kilobase instead of variant count
-Note that you need to rerun PLINK using --extract or --exclude on the
+units.  (Pre-'kb' space is optional, i.e. '--indep-pairwise 500 kb 5 0.5'
-.prune.in/.prune.out file to apply the list to another computation.
+and '--indep-pairwise 500kb 5 0.5' have the same effect.)
+Note that you need to rerun PLINK using --extract or --exclude on the
---r <square | square0 | triangle | inter-chr> <gz | bin | bin4> <spaces>
+.prune.in/.prune.out file to apply the list to another computation.
-<in-phase> <d | dprime | dprime-signed> <with-freqs> <yes-really>
---r2 <square | square0 | triangle | inter-chr> <gz | bin | bin4> <spaces>
+--r <square | square0 | triangle | inter-chr> <gz | bin | bin4> <spaces>
 <in-phase> <d | dprime | dprime-signed> <with-freqs> <yes-really>
-LD statistic reports.  --r yields raw inter-variant correlations, while
+--r2 <square | square0 | triangle | inter-chr> <gz | bin | bin4> <spaces>
---r2 reports their squares.  You can request results for all pairs in
+<in-phase> <d | dprime | dprime-signed> <with-freqs> <yes-really>
-matrix format (if you specify 'bin' or one of the shape modifiers), all
+LD statistic reports.  --r yields raw inter-variant correlations, while
-pairs in table format ('inter-chr'), or a limited window in table format
+--r2 reports their squares.  You can request results for all pairs in
-(default).
+matrix format (if you specify 'bin' or one of the shape modifiers), all
-* The 'gz' modifier causes the output text file to be gzipped.
+pairs in table format ('inter-chr'), or a limited window in table format
-* 'bin' causes the output matrix to be written in double-precision binary
+(default).
-format, while 'bin4' specifics single-precision binary.  The matrix is
+* The 'gz' modifier causes the output text file to be gzipped.
-square if no shape is explicitly specified.
+* 'bin' causes the output matrix to be written in double-precision binary
-* By default, text matrices are tab-delimited; 'spaces' switches this.
+format, while 'bin4' specifics single-precision binary.  The matrix is
-* 'in-phase' adds a column with in-phase allele pairs to table-formatted
+square if no shape is explicitly specified.
-reports.  (This cannot be used with very long allele codes.)
+* By default, text matrices are tab-delimited; 'spaces' switches this.
-* 'dprime' adds the absolute value of Lewontin's D-prime statistic to
+* 'in-phase' adds a column with in-phase allele pairs to table-formatted
-table-formatted reports, and forces both r/r^2 and D-prime to be based on
+reports.  (This cannot be used with very long allele codes.)
-the maximum likelihood solution to the cubic equation discussed in Gaunt
+* 'dprime' adds the absolute value of Lewontin's D-prime statistic to
-T, Rodriguez S, Day I (2007) Cubic exact solutions for the estimation of
+table-formatted reports, and forces both r/r^2 and D-prime to be based on
-pairwise haplotype frequencies.
+the maximum likelihood solution to the cubic equation discussed in Gaunt
-'dprime-signed' keeps the sign, while 'd' skips division by D_{max}.
+T, Rodriguez S, Day I (2007) Cubic exact solutions for the estimation of
-* 'with-freqs' adds MAF columns to table-formatted reports.
+pairwise haplotype frequencies.
-* Since the resulting file can easily be huge, you're required to add the
+'dprime-signed' keeps the sign, while 'd' skips division by D_{max}.
-'yes-really' modifier when requesting an unfiltered, non-distributed all
+* 'with-freqs' adds MAF columns to table-formatted reports.
-pairs computation on more than 400k variants.
+* Since the resulting file can easily be huge, you're required to add the
-* These computations can be subdivided with --parallel (even when the
+'yes-really' modifier when requesting an unfiltered, non-distributed all
-'square' modifier is active).
+pairs computation on more than 400k variants.
---ld [variant ID] [variant ID] <hwe-midp>
+* These computations can be subdivided with --parallel (even when the
-This displays haplotype frequencies, r^2, and D' for a single pair of
+'square' modifier is active).
-variants.  When there are multiple biologically possible solutions to the
+--ld [variant ID] [variant ID] <hwe-midp>
-haplotype frequency cubic equation, all are displayed (instead of just the
+This displays haplotype frequencies, r^2, and D' for a single pair of
-maximum likelihood solution identified by --r/--r2), along with HWE exact
+variants.  When there are multiple biologically possible solutions to the
-test statistics.
+haplotype frequency cubic equation, all are displayed (instead of just the
+maximum likelihood solution identified by --r/--r2), along with HWE exact
---show-tags [filename]
+test statistics.
---show-tags all
-* If a file is specified, list all variants which tag at least one variant
+--show-tags [filename]
-named in the file.  (This will normally be a superset of the original
+--show-tags all
-list, since a variant is considered to tag itself here.)
+* If a file is specified, list all variants which tag at least one variant
-* If 'all' mode is specified, for each variant, each *other* variant which
+named in the file.  (This will normally be a superset of the original
-tags it is reported.
+list, since a variant is considered to tag itself here.)
+* If 'all' mode is specified, for each variant, each *other* variant which
---blocks <no-pheno-req> <no-small-max-span>
+tags it is reported.
-Estimate haplotype blocks, via Haploview's interpretation of the block
-definition suggested by Gabriel S et al. (2002) The Structure of Haplotype
+--blocks <no-pheno-req> <no-small-max-span>
-Blocks in the Human Genome.
+Estimate haplotype blocks, via Haploview's interpretation of the block
-* Normally, samples with missing phenotypes are not considered by this
+definition suggested by Gabriel S et al. (2002) The Structure of Haplotype
-computation; the 'no-pheno-req' modifier lifts this restriction.
+Blocks in the Human Genome.
-* Normally, size-2 blocks may not span more than 20kb, and size-3 blocks
+* Normally, samples with missing phenotypes are not considered by this
-are limited to 30kb.  The 'no-small-max-span' modifier removes these
+computation; the 'no-pheno-req' modifier lifts this restriction.
-limits.
+* Normally, size-2 blocks may not span more than 20kb, and size-3 blocks
-The .blocks file is valid input for PLINK 1.07's --hap command.  However,
+are limited to 30kb.  The 'no-small-max-span' modifier removes these
-the --hap... family of flags has not been reimplemented in PLINK 1.9 due to
+limits.
-poor phasing accuracy relative to other software; for now, we recommend
+The .blocks file is valid input for PLINK 1.07's --hap command.  However,
-using BEAGLE instead of PLINK for case/control haplotype association
+the --hap... family of flags has not been reimplemented in PLINK 1.9 due to
-analysis.  (You can use '--recode beagle' to export data to BEAGLE 3.3.)
+poor phasing accuracy relative to other software; for now, we recommend
-We apologize for the inconvenience, and plan to develop variants of the
+using BEAGLE instead of PLINK for case/control haplotype association
---hap... flags which handle pre-phased data effectively.
+analysis.  (You can use '--recode beagle' to export data to BEAGLE 3.3.)
+We apologize for the inconvenience, and plan to develop variants of the
---distance <square | square0 | triangle> <gz | bin | bin4> <ibs> <1-ibs>
+--hap... flags which handle pre-phased data effectively.
-<allele-ct> <flat-missing>
-Write a lower-triangular tab-delimited table of (weighted) genomic
+--distance <square | square0 | triangle> <gz | bin | bin4> <ibs> <1-ibs>
-distances in allele count units to {output prefix}.dist, and a list of the
+<allele-ct> <flat-missing>
-corresponding sample IDs to {output prefix}.dist.id.  The first row of the
+Write a lower-triangular tab-delimited table of (weighted) genomic
-.dist file contains a single {genome 1-genome 2} distance, the second row
+distances in allele count units to {output prefix}.dist, and a list of the
-has the {genome 1-genome 3} and {genome 2-genome 3} distances in that
+corresponding sample IDs to {output prefix}.dist.id.  The first row of the
-order, etc.
+.dist file contains a single {genome 1-genome 2} distance, the second row
-* It is usually best to perform this calculation on a marker set in
+has the {genome 1-genome 3} and {genome 2-genome 3} distances in that
-approximate linkage equilibrium.
+order, etc.
-* If the 'square' or 'square0' modifier is present, a square matrix is
+* It is usually best to perform this calculation on a marker set in
-written instead; 'square0' fills the upper right triangle with zeroes.
+approximate linkage equilibrium.
-* If the 'gz' modifier is present, a compressed .dist.gz file is written
+* If the 'square' or 'square0' modifier is present, a square matrix is
-instead of a plain text file.
+written instead; 'square0' fills the upper right triangle with zeroes.
-* If the 'bin' modifier is present, a binary (square) matrix of
+* If the 'gz' modifier is present, a compressed .dist.gz file is written
-double-precision floating point values, suitable for loading from R, is
+instead of a plain text file.
-instead written to {output prefix}.dist.bin.  ('bin4' specifies
+* If the 'bin' modifier is present, a binary (square) matrix of
-single-precision numbers instead.)  This can be combined with 'square0'
+double-precision floating point values, suitable for loading from R, is
-if you still want the upper right zeroed out, or 'triangle' if you don't
+instead written to {output prefix}.dist.bin.  ('bin4' specifies
-want to pad the upper right at all.
+single-precision numbers instead.)  This can be combined with 'square0'
-* If the 'ibs' modifier is present, an identity-by-state matrix is written
+if you still want the upper right zeroed out, or 'triangle' if you don't
-to {output prefix}.mibs.  '1-ibs' causes distances expressed as genomic
+want to pad the upper right at all.
-proportions (i.e. 1 - IBS) to be written to {output prefix}.mdist.
+* If the 'ibs' modifier is present, an identity-by-state matrix is written
-Combine with 'allele-ct' if you want to generate the usual .dist file as
+to {output prefix}.mibs.  '1-ibs' causes distances expressed as genomic
-well.
+proportions (i.e. 1 - IBS) to be written to {output prefix}.mdist.
-* By default, distance rescaling in the presence of missing genotype calls
+Combine with 'allele-ct' if you want to generate the usual .dist file as
-is sensitive to allele count distributions: if variant A contributes, on
+well.
-average, twice as much to other pairwise distances as variant B, a
+* By default, distance rescaling in the presence of missing genotype calls
-missing call at variant A will result in twice as large of a missingness
+is sensitive to allele count distributions: if variant A contributes, on
-correction.  To turn this off (because e.g. your missing calls are highly
+average, twice as much to other pairwise distances as variant B, a
-nonrandom), use the 'flat-missing' modifier.
+missing call at variant A will result in twice as large of a missingness
-* The computation can be subdivided with --parallel.
+correction.  To turn this off (because e.g. your missing calls are highly
---distance-matrix
+nonrandom), use the 'flat-missing' modifier.
---ibs-matrix
+* The computation can be subdivided with --parallel.
-These deprecated commands are equivalent to '--distance 1-ibs flat-missing
+--distance-matrix
-square' and '--distance ibs flat-missing square', respectively, except that
+--ibs-matrix
-they generate space- instead of tab-delimited text matrices.
+These deprecated commands are equivalent to '--distance 1-ibs flat-missing
+square' and '--distance ibs flat-missing square', respectively, except that
---make-rel <square | square0 | triangle> <gz | bin | bin4>
+they generate space- instead of tab-delimited text matrices.
-<cov | ibc2 | ibc3>
-Write a lower-triangular variance-standardized realized relationship matrix
+--make-rel <square | square0 | triangle> <gz | bin | bin4>
-to {output prefix}.rel, and corresponding IDs to {output prefix}.rel.id.
+<cov | ibc2 | ibc3>
-* It is usually best to perform this calculation on a marker set in
+Write a lower-triangular variance-standardized realized relationship matrix
-approximate linkage equilibrium.
+to {output prefix}.rel, and corresponding IDs to {output prefix}.rel.id.
-* 'square', 'square0', 'triangle', 'gz', 'bin', and 'bin4' act as they do
+* It is usually best to perform this calculation on a marker set in
-on --distance.
+approximate linkage equilibrium.
-* The 'cov' modifier removes the variance standardization step, causing a
+* 'square', 'square0', 'triangle', 'gz', 'bin', and 'bin4' act as they do
-covariance matrix to be calculated instead.
+on --distance.
-* By default, the diagonal elements in the relationship matrix are based on
+* The 'cov' modifier removes the variance standardization step, causing a
---ibc's Fhat1; use the 'ibc2' or 'ibc3' modifiers to base them on Fhat2
+covariance matrix to be calculated instead.
-or Fhat3 instead.
+* By default, the diagonal elements in the relationship matrix are based on
-* The computation can be subdivided with --parallel.
+--ibc's Fhat1; use the 'ibc2' or 'ibc3' modifiers to base them on Fhat2
---make-grm-gz <no-gz> <cov | ibc2 | ibc3>
+or Fhat3 instead.
---make-grm-bin <cov | ibc2 | ibc3>
+* The computation can be subdivided with --parallel.
---make-grm-gz writes the relationships in GCTA's original gzipped list
+--make-grm-gz <no-gz> <cov | ibc2 | ibc3>
-format, which describes one pair per line, while --make-grm-bin writes them
+--make-grm-bin <cov | ibc2 | ibc3>
-in GCTA 1.1+'s single-precision triangular binary format.  Note that these
+--make-grm-gz writes the relationships in GCTA's original gzipped list
-formats explicitly report the number of valid observations (where neither
+format, which describes one pair per line, while --make-grm-bin writes them
-sample has a missing call) for each pair, which is useful input for some
+in GCTA 1.1+'s single-precision triangular binary format.  Note that these
-scripts.
+formats explicitly report the number of valid observations (where neither
-These computations can be subdivided with --parallel.
+sample has a missing call) for each pair, which is useful input for some
+scripts.
---rel-cutoff {val}
+These computations can be subdivided with --parallel.
-(alias: --grm-cutoff)
-Exclude one member of each pair of samples with relatedness greater than
+--rel-cutoff {val}
-the given cutoff value (default 0.025).  If no later operation will cause
+(alias: --grm-cutoff)
-the list of remaining samples to be written to disk, this will save it to
+Exclude one member of each pair of samples with relatedness greater than
-{output prefix}.rel.id.
+the given cutoff value (default 0.025).  If no later operation will cause
-Note that maximizing the remaining sample size is equivalent to the NP-hard
+the list of remaining samples to be written to disk, this will save it to
-maximum independent set problem, so we use a greedy algorithm instead of
+{output prefix}.rel.id.
-guaranteeing optimality.  (Use the --make-rel and --keep/--remove flags if
+Note that maximizing the remaining sample size is equivalent to the NP-hard
-you want to try to do better.)
+maximum independent set problem, so we use a greedy algorithm instead of
+guaranteeing optimality.  (Use the --make-rel and --keep/--remove flags if
---ibs-test {permutation count}
+you want to try to do better.)
---groupdist {iters} {d}
-Given case/control phenotype data, these commands consider three subsets of
+--ibs-test {permutation count}
-the distance matrix: pairs of affected samples, affected-unaffected pairs,
+--groupdist {iters} {d}
-and pairs of unaffected samples.  Each of these subsets has a distribution
+Given case/control phenotype data, these commands consider three subsets of
-of pairwise genomic distances; --ibs-test uses permutation to estimate
+the distance matrix: pairs of affected samples, affected-unaffected pairs,
-p-values re: which types of pairs are most similar, while --groupdist
+and pairs of unaffected samples.  Each of these subsets has a distribution
-focuses on the differences between the centers of these distributions and
+of pairwise genomic distances; --ibs-test uses permutation to estimate
-estimates standard errors via delete-d jackknife.
+p-values re: which types of pairs are most similar, while --groupdist
+focuses on the differences between the centers of these distributions and
---regress-distance {iters} {d}
+estimates standard errors via delete-d jackknife.
-Linear regression of pairwise genomic distances on pairwise average
-phenotypes and vice versa, using delete-d jackknife for standard errors.  A
+--regress-distance {iters} {d}
-scalar phenotype is required.
+Linear regression of pairwise genomic distances on pairwise average
-* With less than two parameters, d is set to {number of people}^0.6 rounded
+phenotypes and vice versa, using delete-d jackknife for standard errors.  A
-down.  With no parameters, 100k iterations are run.
+scalar phenotype is required.
---regress-rel {iters} {d}
+* With less than two parameters, d is set to {number of people}^0.6 rounded
-Linear regression of pairwise genomic relationships on pairwise average
+down.  With no parameters, 100k iterations are run.
-phenotypes, and vice versa.  Defaults for iters and d are the same as for
+--regress-rel {iters} {d}
---regress-distance.
+Linear regression of pairwise genomic relationships on pairwise average
+phenotypes, and vice versa.  Defaults for iters and d are the same as for
---genome <gz> <rel-check> <full> <unbounded> <nudge>
+--regress-distance.
-Generate an identity-by-descent report.
-* It is usually best to perform this calculation on a marker set in
+--genome <gz> <rel-check> <full> <unbounded> <nudge>
-approximate linkage equilibrium.
+Generate an identity-by-descent report.
-* The 'rel-check' modifier excludes pairs of samples with different FIDs
+* It is usually best to perform this calculation on a marker set in
-from the final report.
+approximate linkage equilibrium.
-* 'full' adds raw pairwise comparison data to the report.
+* The 'rel-check' modifier excludes pairs of samples with different FIDs
-* The P(IBD=0/1/2) estimator employed by this command sometimes yields
+from the final report.
-numbers outside the range [0,1]; by default, these are clipped.  The
+* 'full' adds raw pairwise comparison data to the report.
-'unbounded' modifier turns off this clipping.
+* The P(IBD=0/1/2) estimator employed by this command sometimes yields
-* Then, when PI_HAT^2 < P(IBD=2), 'nudge' adjusts the final P(IBD=0/1/2)
+numbers outside the range [0,1]; by default, these are clipped.  The
-estimates to a theoretically possible configuration.
+'unbounded' modifier turns off this clipping.
-* The computation can be subdivided with --parallel.
+* Then, when PI_HAT^2 < P(IBD=2), 'nudge' adjusts the final P(IBD=0/1/2)
+estimates to a theoretically possible configuration.
---homozyg <group | group-verbose> <consensus-match> <extend>
+* The computation can be subdivided with --parallel.
-<subtract-1-from-lengths>
---homozyg-snp [min var count]
+--homozyg <group | group-verbose> <consensus-match> <extend>
---homozyg-kb [min length]
+<subtract-1-from-lengths>
---homozyg-density [max inverse density (kb/var)]
+--homozyg-snp [min var count]
---homozyg-gap [max internal gap kb length]
+--homozyg-kb [min length]
---homozyg-het [max hets]
+--homozyg-density [max inverse density (kb/var)]
---homozyg-window-snp [scanning window size]
+--homozyg-gap [max internal gap kb length]
---homozyg-window-het [max hets in scanning window hit]
+--homozyg-het [max hets]
---homozyg-window-missing [max missing calls in scanning window hit]
+--homozyg-window-snp [scanning window size]
---homozyg-window-threshold [min scanning window hit rate]
+--homozyg-window-het [max hets in scanning window hit]
-These commands request a set of run-of-homozygosity reports, and allow you
+--homozyg-window-missing [max missing calls in scanning window hit]
-to customize how they are generated.
+--homozyg-window-threshold [min scanning window hit rate]
-* If you're satisfied with all the default settings described below, just
+These commands request a set of run-of-homozygosity reports, and allow you
-use --homozyg with no modifiers.  Otherwise, --homozyg lets you change a
+to customize how they are generated.
-few binary settings:
+* If you're satisfied with all the default settings described below, just
-* 'group{-verbose}' adds a report on pools of overlapping runs of
+use --homozyg with no modifiers.  Otherwise, --homozyg lets you change a
-homozygosity.  (Automatically set when --homozyg-match is present.)
+few binary settings:
-* With 'group{-verbose}', 'consensus-match' causes pairwise segmental
+* 'group{-verbose}' adds a report on pools of overlapping runs of
-matches to be called based on the variants in the pool's consensus
+homozygosity.  (Automatically set when --homozyg-match is present.)
-segment, rather than the variants in the pairwise intersection.
+* With 'group{-verbose}', 'consensus-match' causes pairwise segmental
-* Due to how the scanning window algorithm works, it is possible for a
+matches to be called based on the variants in the pool's consensus
-reported ROH to be adjacent to a few homozygous variants.  The 'extend'
+segment, rather than the variants in the pairwise intersection.
-modifier causes them to be included in the reported ROH if that
+* Due to how the scanning window algorithm works, it is possible for a
-wouldn't cause a violation of the --homozyg-density bound.
+reported ROH to be adjacent to a few homozygous variants.  The 'extend'
-* By default, segment bp lengths are calculated as [end bp position] -
+modifier causes them to be included in the reported ROH if that
-[start bp position] + 1.  Therefore, reports normally differ slightly
+wouldn't cause a violation of the --homozyg-density bound.
-from PLINK 1.07, which does not add 1 at the end.  For testing
+* By default, segment bp lengths are calculated as [end bp position] -
-purposes, you can use the 'subtract-1-from-lengths' modifier to apply
+[start bp position] + 1.  Therefore, reports normally differ slightly
-the old formula.
+from PLINK 1.07, which does not add 1 at the end.  For testing
-* By default, only runs of homozygosity containing at least 100 variants,
+purposes, you can use the 'subtract-1-from-lengths' modifier to apply
-and of total length >= 1000 kilobases, are noted.  You can change these
+the old formula.
-minimums with --homozyg-snp and --homozyg-kb, respectively.
+* By default, only runs of homozygosity containing at least 100 variants,
-* By default, a ROH must have at least one variant per 50 kb on average;
+and of total length >= 1000 kilobases, are noted.  You can change these
-change this bound with --homozyg-density.
+minimums with --homozyg-snp and --homozyg-kb, respectively.
-* By default, if two consecutive variants are more than 1000 kb apart, they
+* By default, a ROH must have at least one variant per 50 kb on average;
-cannot be in the same ROH; change this bound with --homozyg-gap.
+change this bound with --homozyg-density.
-* By default, a ROH can contain an unlimited number of heterozygous calls;
+* By default, if two consecutive variants are more than 1000 kb apart, they
-you can impose a limit with --homozyg-het.
+cannot be in the same ROH; change this bound with --homozyg-gap.
-* By default, the scanning window contains 50 variants; change this with
+* By default, a ROH can contain an unlimited number of heterozygous calls;
---homozyg-window-snp.
+you can impose a limit with --homozyg-het.
-* By default, a scanning window hit can contain at most 1 heterozygous
+* By default, the scanning window contains 50 variants; change this with
-call and 5 missing calls; change these limits with --homozyg-window-het
+--homozyg-window-snp.
-and --homozyg-window-missing, respectively.
+* By default, a scanning window hit can contain at most 1 heterozygous
-* By default, for a variant to be eligible for inclusion in a ROH, the hit
+call and 5 missing calls; change these limits with --homozyg-window-het
-rate of all scanning windows containing the variant must be at least
+and --homozyg-window-missing, respectively.
-0.05; change this threshold with --homozyg-window-threshold.
+* By default, for a variant to be eligible for inclusion in a ROH, the hit
+rate of all scanning windows containing the variant must be at least
---cluster <cc> <group-avg | old-tiebreaks> <missing> <only2>
+0.05; change this threshold with --homozyg-window-threshold.
-Cluster samples using a pairwise similarity statistic (normally IBS).
-* The 'cc' modifier forces every cluster to have at least one case and one
+--cluster <cc> <group-avg | old-tiebreaks> <missing> <only2>
-control.
+Cluster samples using a pairwise similarity statistic (normally IBS).
-* The 'group-avg' modifier causes clusters to be joined based on average
+* The 'cc' modifier forces every cluster to have at least one case and one
-instead of minimum pairwise similarity.
+control.
-* The 'missing' modifier causes clustering to be based on
+* The 'group-avg' modifier causes clusters to be joined based on average
-identity-by-missingness instead of identity-by-state, and writes a
+instead of minimum pairwise similarity.
-space-delimited identity-by-missingness matrix to disk.
+* The 'missing' modifier causes clustering to be based on
-* The 'only2' modifier causes only a .cluster2 file (which is valid input
+identity-by-missingness instead of identity-by-state, and writes a
-for --within) to be written; otherwise 2 other files will be produced.
+space-delimited identity-by-missingness matrix to disk.
-* By default, IBS ties are not broken in the same manner as PLINK 1.07, so
+* The 'only2' modifier causes only a .cluster2 file (which is valid input
-final cluster solutions tend to differ.  This is generally harmless.
+for --within) to be written; otherwise 2 other files will be produced.
-However, to simplify testing, you can use the 'old-tiebreaks' modifier to
+* By default, IBS ties are not broken in the same manner as PLINK 1.07, so
-force emulation of the old algorithm.
+final cluster solutions tend to differ.  This is generally harmless.
+However, to simplify testing, you can use the 'old-tiebreaks' modifier to
---pca {count} <header> <tabs> <var-wts>
+force emulation of the old algorithm.
-Calculates a variance-standardized relationship matrix (use
---make-rel/--make-grm-gz/--make-grm-bin to dump it), and extracts the top
+--pca {count} <header> <tabs> <var-wts>
-20 principal components.
+Calculates a variance-standardized relationship matrix (use
-* It is usually best to perform this calculation on a marker set in
+--make-rel/--make-grm-gz/--make-grm-bin to dump it), and extracts the top
-approximate linkage equilibrium.
+20 principal components.
-* You can change the number of PCs by passing a numeric parameter.
+* It is usually best to perform this calculation on a marker set in
-* The 'header' modifier adds a header line to the .eigenvec output file.
+approximate linkage equilibrium.
-(For compatibility with the GCTA flag of the same name, the default is no
+* You can change the number of PCs by passing a numeric parameter.
-header line.)
+* The 'header' modifier adds a header line to the .eigenvec output file.
-* The 'tabs' modifier causes the .eigenvec file(s) to be tab-delimited.
+(For compatibility with the GCTA flag of the same name, the default is no
-* The 'var-wts' modifier requests an additional .eigenvec.var file with PCs
+header line.)
-expressed as variant weights instead of sample weights.
+* The 'tabs' modifier causes the .eigenvec file(s) to be tab-delimited.
+* The 'var-wts' modifier requests an additional .eigenvec.var file with PCs
---neighbour [n1] [n2]
+expressed as variant weights instead of sample weights.
-(alias: --neighbor)
-Report IBS distances from each sample to their n1th- to n2th-nearest
+--neighbour [n1] [n2]
-neighbors, associated Z-scores, and the identities of those neighbors.
+(alias: --neighbor)
-Useful for outlier detection.
+Report IBS distances from each sample to their n1th- to n2th-nearest
+neighbors, associated Z-scores, and the identities of those neighbors.
---assoc <perm | mperm=[value]> <perm-count> <fisher | fisher-midp> <counts>
+Useful for outlier detection.
-<set-test>
---assoc <perm | mperm=[value]> <perm-count> <qt-means> <lin> <set-test>
+--assoc <perm | mperm=[value]> <perm-count> <fisher | fisher-midp> <counts>
---model <perm | mperm=[value]> <perm-count>
+<set-test>
-<fisher | fisher-midp | trend-only> <set-test>
+--assoc <perm | mperm=[value]> <perm-count> <qt-means> <lin> <set-test>
-<dom | rec | gen | trend>
+--model <perm | mperm=[value]> <perm-count>
-Basic association analysis report.
+<fisher | fisher-midp | trend-only> <set-test>
-Given a case/control phenotype, --assoc performs a 1df chi-square allelic
+<dom | rec | gen | trend>
-test, while --model performs 4 other tests as well (1df dominant gene
+Basic association analysis report.
-action, 1df recessive gene action, 2df genotypic, Cochran-Armitage trend).
+Given a case/control phenotype, --assoc performs a 1df chi-square allelic
-* With 'fisher'/'fisher-midp', Fisher's exact test is used to generate
+test, while --model performs 4 other tests as well (1df dominant gene
-p-values.  'fisher-midp' also applies Lancaster's mid-p adjustment.
+action, 1df recessive gene action, 2df genotypic, Cochran-Armitage trend).
-* 'perm' causes an adaptive permutation test to be performed.
+* With 'fisher'/'fisher-midp', Fisher's exact test is used to generate
-* 'mperm=[value]' causes a max(T) permutation test with the specified
+p-values.  'fisher-midp' also applies Lancaster's mid-p adjustment.
-number of replications to be performed.
+* 'perm' causes an adaptive permutation test to be performed.
-* 'perm-count' causes the permutation test report to include counts instead
+* 'mperm=[value]' causes a max(T) permutation test with the specified
-of frequencies.
+number of replications to be performed.
-* 'counts' causes --assoc to report allele counts instead of frequencies.
+* 'perm-count' causes the permutation test report to include counts instead
-* 'set-test' tests the significance of variant sets.  Requires permutation;
+of frequencies.
-can be customized with --set-p/--set-r2/--set-max.
+* 'counts' causes --assoc to report allele counts instead of frequencies.
-* 'dom', 'rec', 'gen', and 'trend' force the corresponding test to be used
+* 'set-test' tests the significance of variant sets.  Requires permutation;
-as the basis for --model permutation.  (By default, the most significant
+can be customized with --set-p/--set-r2/--set-max.
-result among the allelic, dominant, and recessive tests is used.)
+* 'dom', 'rec', 'gen', and 'trend' force the corresponding test to be used
-* 'trend-only' causes only the trend test to be performed.
+as the basis for --model permutation.  (By default, the most significant
-Given a quantitative phenotype, --assoc normally performs a Wald test.
+result among the allelic, dominant, and recessive tests is used.)
-* In this case, the 'qt-means' modifier causes trait means and standard
+* 'trend-only' causes only the trend test to be performed.
-deviations stratified by genotype to be reported as well.
+Given a quantitative phenotype, --assoc normally performs a Wald test.
-* 'lin' causes the Lin statistic to be computed, and makes it the basis for
+* In this case, the 'qt-means' modifier causes trait means and standard
-multiple-testing corrections and permutation tests.
+deviations stratified by genotype to be reported as well.
-Several other flags (most notably, --aperm) can be used to customize the
+* 'lin' causes the Lin statistic to be computed, and makes it the basis for
-permutation test.
+multiple-testing corrections and permutation tests.
+Several other flags (most notably, --aperm) can be used to customize the
---mh <perm | mperm=[value]> <perm-count> <set-test>
+permutation test.
-(alias: --cmh)
---bd <perm | perm-bd | mperm=[value]> <perm-count> <set-test>
+--mh <perm | mperm=[value]> <perm-count> <set-test>
---mh2
+(alias: --cmh)
---homog
+--bd <perm | perm-bd | mperm=[value]> <perm-count> <set-test>
-Given a case/control phenotype and a set of clusters, --mh computes 2x2xK
+--mh2
-Cochran-Mantel-Haenszel statistics for each variant, while --bd also
+--homog
-performs the Breslow-Day test for odds ratio homogeneity.  Permutation and
+Given a case/control phenotype and a set of clusters, --mh computes 2x2xK
-variant set testing based on the CMH (default) or Breslow-Day (when
+Cochran-Mantel-Haenszel statistics for each variant, while --bd also
-'perm-bd' is present) statistic are supported.
+performs the Breslow-Day test for odds ratio homogeneity.  Permutation and
-The following similar analyses are also available:
+variant set testing based on the CMH (default) or Breslow-Day (when
-* --mh2 swaps the roles of case/control status and cluster membership,
+'perm-bd' is present) statistic are supported.
-performing a phenotype-stratified IxJxK Cochran-Mantel-Haenszel test on
+The following similar analyses are also available:
-association between cluster assignments and genotypes.
+* --mh2 swaps the roles of case/control status and cluster membership,
-* --homog executes an alternative to the Breslow-Day test, based on
+performing a phenotype-stratified IxJxK Cochran-Mantel-Haenszel test on
-partitioning of the chi-square statistic.
+association between cluster assignments and genotypes.
+* --homog executes an alternative to the Breslow-Day test, based on
---gxe {covariate index}
+partitioning of the chi-square statistic.
-Given both a quantitative phenotype and a case/control covariate loaded
-with --covar defining two groups, --gxe compares the regression coefficient
+--gxe {covariate index}
-derived from considering only members of one group to the regression
+Given both a quantitative phenotype and a case/control covariate loaded
-coefficient derived from considering only members of the other.  By
+with --covar defining two groups, --gxe compares the regression coefficient
-default, the first covariate in the --covar file defines the groups; use
+derived from considering only members of one group to the regression
-e.g. '--gxe 3' to base them on the third covariate instead.
+coefficient derived from considering only members of the other.  By
+default, the first covariate in the --covar file defines the groups; use
---linear <perm | mperm=[value]> <perm-count> <set-test>
+e.g. '--gxe 3' to base them on the third covariate instead.
-<genotypic | hethom | dominant | recessive | no-snp> <hide-covar>
-<sex | no-x-sex> <interaction> <beta> <standard-beta> <intercept>
+--linear <perm | mperm=[value]> <perm-count> <set-test>
---logistic <perm | mperm=[value]> <perm-count> <set-test>
 <genotypic | hethom | dominant | recessive | no-snp> <hide-covar>
-<sex | no-x-sex> <interaction> <beta> <intercept>
+<sex | no-x-sex> <interaction> <beta> <standard-beta> <intercept>
-Multi-covariate association analysis on a quantitative (--linear) or
+--logistic <perm | mperm=[value]> <perm-count> <set-test>
-case/control (--logistic) phenotype.  Normally used with --covar.
+<genotypic | hethom | dominant | recessive | no-snp> <hide-covar>
-* 'perm' normally causes an adaptive permutation test to be performed on
+<sex | no-x-sex> <interaction> <beta> <intercept>
-the main effect, while 'mperm=[value]' starts a max(T) permutation test.
+Multi-covariate association analysis on a quantitative (--linear) or
-* 'perm-count' causes the permutation test report to include counts instead
+case/control (--logistic) phenotype.  Normally used with --covar.
-of frequencies.
+* 'perm' normally causes an adaptive permutation test to be performed on
-* 'set-test' tests the significance of variant sets.  Requires permutation;
+the main effect, while 'mperm=[value]' starts a max(T) permutation test.
-can be customized with --set-p/--set-r2/--set-max.
+* 'perm-count' causes the permutation test report to include counts instead
-* The 'genotypic' modifier adds an additive effect/dominance deviation 2df
+of frequencies.
-joint test (0/1/2 and 0/1/0 coding), while 'hethom' uses 0/0/1 and 0/1/0
+* 'set-test' tests the significance of variant sets.  Requires permutation;
-coding instead.  If permutation is also requested, these modifiers cause
+can be customized with --set-p/--set-r2/--set-max.
-permutation to be based on the joint test.
+* The 'genotypic' modifier adds an additive effect/dominance deviation 2df
-* 'dominant' and 'recessive' specify a model assuming full dominance or
+joint test (0/1/2 and 0/1/0 coding), while 'hethom' uses 0/0/1 and 0/1/0
-recessiveness, respectively, for the A1 allele.
+coding instead.  If permutation is also requested, these modifiers cause
-* 'no-snp' causes regression to be performed only on the phenotype and the
+permutation to be based on the joint test.
-covariates, without reference to genomic data.  If permutation is also
+* 'dominant' and 'recessive' specify a model assuming full dominance or
-requested, results are reported for all covariates.
+recessiveness, respectively, for the A1 allele.
-* 'hide-covar' removes covariate-specific lines from the report.
+* 'no-snp' causes regression to be performed only on the phenotype and the
-* By default, sex (male = 1, female = 0) is automatically added as a
+covariates, without reference to genomic data.  If permutation is also
-covariate on X chromosome variants, and nowhere else.  The 'sex' modifier
+requested, results are reported for all covariates.
-causes it to be added everywhere, while 'no-x-sex' excludes it.
+* 'hide-covar' removes covariate-specific lines from the report.
-* 'interaction' adds genotype x covariate interactions to the model.  This
+* By default, sex (male = 1, female = 0) is automatically added as a
-cannot be used with the usual permutation tests; use --tests to define
+covariate on X chromosome variants, and nowhere else.  The 'sex' modifier
-the permutation test statistic instead.
+causes it to be added everywhere, while 'no-x-sex' excludes it.
-* 'intercept' causes intercepts to be included in the main report.
+* 'interaction' adds genotype x covariate interactions to the model.  This
-* For logistic regressions, the 'beta' modifier causes regression
+cannot be used with the usual permutation tests; use --tests to define
-coefficients instead of odds ratios to be reported.
+the permutation test statistic instead.
-* With --linear, the 'standard-beta' modifier standardizes the phenotype
+* 'intercept' causes intercepts to be included in the main report.
-and all predictors to zero mean and unit variance before regression.
+* For logistic regressions, the 'beta' modifier causes regression
+coefficients instead of odds ratios to be reported.
---dosage [allele dosage file] <noheader> <skip0=[i]> <skip1=[j]> <skip2=[k]>
+* With --linear, the 'standard-beta' modifier standardizes the phenotype
-<dose1> <format=[m]> <Zout> <occur | standard-beta> <sex>
+and all predictors to zero mean and unit variance before regression.
-<case-control-freqs>
---dosage [list file] list <sepheader | noheader> <skip0=[i]> <skip1=[j]>
+--dosage [allele dosage file] <noheader> <skip0=[i]> <skip1=[j]> <skip2=[k]>
-<skip2=[k]> <dose1> <format=[m]> <Zout> <occur | standard-beta>
+<dose1> <format=[m]> <Zout> <occur | standard-beta> <sex>
-<sex> <case-control-freqs>
+<case-control-freqs>
---write-dosage
+--dosage [list file] list <sepheader | noheader> <skip0=[i]> <skip1=[j]>
-Process (possibly gzipped) text files with variant-major allelic dosage
+<skip2=[k]> <dose1> <format=[m]> <Zout> <occur | standard-beta>
-data.  This cannot be used with a regular input fileset; instead, you must
+<sex> <case-control-freqs>
-*only* specify a .fam and possibly a .map file, and you can't specify any
+--write-dosage
-other commands.
+Process (possibly gzipped) text files with variant-major allelic dosage
-* PLINK 2.0 will have first-class support for genotype probabilities.  An
+data.  This cannot be used with a regular input fileset; instead, you must
-equivalent data import flag will be provided then, and --dosage will be
+*only* specify a .fam and possibly a .map file, and you can't specify any
-retired.
+other commands.
-* By default, --dosage assumes that only one allelic dosage file should be
+* PLINK 2.0 will have first-class support for genotype probabilities.  An
-loaded.  To specify multiple files,
+equivalent data import flag will be provided then, and --dosage will be
-1. create a master list with one entry per line.  There are normally two
+retired.
-supported formats for this list: just a filename per line, or variant
+* By default, --dosage assumes that only one allelic dosage file should be
-batch numbers in the first column and filenames in the second.
+loaded.  To specify multiple files,
-2. Provide the name of that list as the first --dosage parameter.
+1. create a master list with one entry per line.  There are normally two
-3. Add the 'list' modifier.
+supported formats for this list: just a filename per line, or variant
-* By default, --dosage assumes the allelic dosage file(s) contain a header
+batch numbers in the first column and filenames in the second.
-line, which has 'SNP' in column i+1, 'A1' in column i+j+2, 'A2' in column
+2. Provide the name of that list as the first --dosage parameter.
-i+j+3, and sample FID/IIDs starting from column i+j+k+4.  (i/j/k are
+3. Add the 'list' modifier.
-normally zero, but can be changed with 'skip0', 'skip1', and 'skip2'
+* By default, --dosage assumes the allelic dosage file(s) contain a header
-respectively.)  If such a header line is not present,
+line, which has 'SNP' in column i+1, 'A1' in column i+j+2, 'A2' in column
-* when all samples appear in the same order as they do in the .fam file,
+i+j+3, and sample FID/IIDs starting from column i+j+k+4.  (i/j/k are
-you can use the 'noheader' modiifer.
+normally zero, but can be changed with 'skip0', 'skip1', and 'skip2'
-* Otherwise, use the 'sepheader' modifier, and append sample ID filenames
+respectively.)  If such a header line is not present,
-to your 'list' file entries.
+* when all samples appear in the same order as they do in the .fam file,
-* The 'format' modifier lets you specify the number of values used to
+you can use the 'noheader' modiifer.
-represent each dosage.  'format=1' normally indicates a single 0..2 A1
+* Otherwise, use the 'sepheader' modifier, and append sample ID filenames
-expected count; 'dose1' modifies this to a 0..1 frequency.  'format=2'
+to your 'list' file entries.
-(the default) indicates a 0..1 homozygous A1 likelihood followed by a
+* The 'format' modifier lets you specify the number of values used to
-0..1 het likelihood, while 'format=3' indicates 0..1 hom A1, 0..1 het,
+represent each dosage.  'format=1' normally indicates a single 0..2 A1
-0..1 hom A2.
+expected count; 'dose1' modifies this to a 0..1 frequency.  'format=2'
-* 'Zout' causes the output file to be gzipped.
+(the default) indicates a 0..1 homozygous A1 likelihood followed by a
-* Normally, an association analysis is performed.  'standard-beta' and
+0..1 het likelihood, while 'format=3' indicates 0..1 hom A1, 0..1 het,
-'sex' behave as they are supposed to with --linear/--logistic.
+0..1 hom A2.
-'case-control-freqs' causes case and control allele frequencies to be
+* 'Zout' causes the output file to be gzipped.
-reported separately.
+* Normally, an association analysis is performed.  'standard-beta' and
-* There are three alternate modes which cause the association analysis to
+'sex' behave as they are supposed to with --linear/--logistic.
-be skipped.
+'case-control-freqs' causes case and control allele frequencies to be
-* 'occur' requests a simple variant occurrence report.
+reported separately.
-* --write-dosage causes a simple merged file matching the 'format'
+* There are three alternate modes which cause the association analysis to
-specification (not including 'dose1') to be generated.
+be skipped.
-* --score applies a linear scoring system to the dosages.
+* 'occur' requests a simple variant occurrence report.
+* --write-dosage causes a simple merged file matching the 'format'
---lasso [h2 estimate] {min lambda} <report-zeroes>
+specification (not including 'dose1') to be generated.
-Estimate variant effect sizes via LASSO regression.  You must provide an
+* --score applies a linear scoring system to the dosages.
-additive heritability estimate to calibrate the regression.
-Note that this method may require a very large sample size (e.g. hundreds
+--lasso [h2 estimate] {min lambda} <report-zeroes>
-of thousands) to be effective on complex polygenic traits.
+Estimate variant effect sizes via LASSO regression.  You must provide an
+additive heritability estimate to calibrate the regression.
---test-missing <perm | mperm=[value]> <perm-count> <midp>
+Note that this method may require a very large sample size (e.g. hundreds
-Check for association between missingness and case/control status, using
+of thousands) to be effective on complex polygenic traits.
-Fisher's exact test.  The 'midp' modifier causes Lancaster's mid-p
-adjustment to be applied.
+--test-missing <perm | mperm=[value]> <perm-count> <midp>
+Check for association between missingness and case/control status, using
---make-perm-pheno [ct]
+Fisher's exact test.  The 'midp' modifier causes Lancaster's mid-p
-Generate phenotype permutations and write them to disk, without invoking an
+adjustment to be applied.
-association test.
+--make-perm-pheno [ct]
---tdt <exact | exact-midp | poo> <perm | mperm=[value]> <perm-count>
+Generate phenotype permutations and write them to disk, without invoking an
-<parentdt1 | parentdt2 | pat | mat> <set-test>
+association test.
-Report transmission disequilibrium test statistics, given case/control
-phenotypes and pedigree information.
+--tdt <exact | exact-midp | poo> <perm | mperm=[value]> <perm-count>
-* A Mendel error check is performed before the main tests; offending
+<parentdt1 | parentdt2 | pat | mat> <set-test>
-genotypes are treated as missing by this analysis.
+Report transmission disequilibrium test statistics, given case/control
-* By default, the basic TDT p-value is based on a chi-square test unless
+phenotypes and pedigree information.
-you request the exact binomial test with 'exact' or 'exact-midp'.
+* A Mendel error check is performed before the main tests; offending
-* 'perm'/'mperm=[value]' requests a family-based adaptive or max(T)
+genotypes are treated as missing by this analysis.
-permutation test.  By default, the permutation test statistic is the
+* By default, the basic TDT p-value is based on a chi-square test unless
-basic TDT p-value; 'parentdt1'/'parentdt2' cause parenTDT or combined
+you request the exact binomial test with 'exact' or 'exact-midp'.
-test p-values, respectively, to be considered instead.
+* 'perm'/'mperm=[value]' requests a family-based adaptive or max(T)
-* 'set-test' tests the significance of variant sets.  This cannot be used
+permutation test.  By default, the permutation test statistic is the
-with exact tests for now.
+basic TDT p-value; 'parentdt1'/'parentdt2' cause parenTDT or combined
-The 'poo' modifier causes a parent-of-origin analysis to be performed
+test p-values, respectively, to be considered instead.
-instead, with transmissions from heterozygous fathers and heterozygous
+* 'set-test' tests the significance of variant sets.  This cannot be used
-mothers considered separately.
+with exact tests for now.
-* The parent-of-origin analysis does not currently support exact tests.
+The 'poo' modifier causes a parent-of-origin analysis to be performed
-* By default, the permutation test statistic is the absolute
+instead, with transmissions from heterozygous fathers and heterozygous
-parent-of-origin test Z score; 'pat'/'mat' cause paternal or maternal TDT
+mothers considered separately.
-chi-square statistics, respectively, to be considered instead.
+* The parent-of-origin analysis does not currently support exact tests.
+* By default, the permutation test statistic is the absolute
---qfam <perm | mperm=[value]> <perm-count> <emp-se>
+parent-of-origin test Z score; 'pat'/'mat' cause paternal or maternal TDT
---qfam-parents <perm | mperm=[value]> <perm-count> <emp-se>
+chi-square statistics, respectively, to be considered instead.
---qfam-between <perm | mperm=[value]> <perm-count> <emp-se>
---qfam-total <perm | mperm=[value]> <perm-count> <emp-se>
+--qfam <perm | mperm=[value]> <perm-count> <emp-se>
-QFAM family-based association test for quantitative traits.
+--qfam-parents <perm | mperm=[value]> <perm-count> <emp-se>
-* A Mendel error check is performed before the main tests; offending
+--qfam-between <perm | mperm=[value]> <perm-count> <emp-se>
-genotypes are treated as missing by this analysis.
+--qfam-total <perm | mperm=[value]> <perm-count> <emp-se>
-* This procedure requires permutation.  'perm' and 'perm-count' have the
+QFAM family-based association test for quantitative traits.
-usual meanings.  However, 'mperm=[value]' just specifies a fixed number
+* A Mendel error check is performed before the main tests; offending
-of permutations; the method does not support a proper max(T) test.
+genotypes are treated as missing by this analysis.
-* The 'emp-se' modifier adds BETA and EMP_SE (empirical standard error for
+* This procedure requires permutation.  'perm' and 'perm-count' have the
-beta) fields to the .perm output file.
+usual meanings.  However, 'mperm=[value]' just specifies a fixed number
+of permutations; the method does not support a proper max(T) test.
---annotate [PLINK report] <attrib=[file]> <ranges=[file]> <filter=[file]>
+* The 'emp-se' modifier adds BETA and EMP_SE (empirical standard error for
-<snps=[file]> <NA | prune> <block> <subset=[file]> <minimal>
+beta) fields to the .perm output file.
-<distance>
-Add annotations to a variant-based PLINK report.  This requires an
+--annotate [PLINK report] <attrib=[file]> <ranges=[file]> <filter=[file]>
-annotation source:
+<snps=[file]> <NA | prune> <block> <subset=[file]> <minimal>
-* 'attrib=[file]' specifies a (possibly gzipped) attribute file.
+<distance>
-* 'ranges=[file]' specifies a gene/range list file.
+Add annotations to a variant-based PLINK report.  This requires an
-(Both source types can be specified simultaneously.)  The following options
+annotation source:
-are also supported:
+* 'attrib=[file]' specifies a (possibly gzipped) attribute file.
-* 'filter=[file]' causes only variants within one of the ranges in the file
+* 'ranges=[file]' specifies a gene/range list file.
-to be included in the new report.
+(Both source types can be specified simultaneously.)  The following options
-* 'snps=[file]' causes only variants named in the file to be included in
+are also supported:
-the new report.
+* 'filter=[file]' causes only variants within one of the ranges in the file
-* The 'NA' modifier causes unannotated variants to have 'NA' instead of '.'
+to be included in the new report.
-in the new report's ANNOT column, while the 'prune' modifier excludes
+* 'snps=[file]' causes only variants named in the file to be included in
-them entirely.
+the new report.
-* The 'block' modifier replaces the single ANNOT column with a 0/1-coded
+* The 'NA' modifier causes unannotated variants to have 'NA' instead of '.'
-column for each possible annotation.
+in the new report's ANNOT column, while the 'prune' modifier excludes
-* With 'ranges',
+them entirely.
-* 'subset=[file]' causes only intervals named in the subset file to be
+* The 'block' modifier replaces the single ANNOT column with a 0/1-coded
-loaded from the ranges file.
+column for each possible annotation.
-* interval annotations normally come with a parenthesized signed distance
+* With 'ranges',
-to the interval boundary (0 if the variant is located inside the
+* 'subset=[file]' causes only intervals named in the subset file to be
-interval; this is always true without --border).  They can be excluded
+loaded from the ranges file.
-with the 'minimal' modifier.
+* interval annotations normally come with a parenthesized signed distance
-* the 'distance' modifier adds 'DIST' and 'SGN' columns describing signed
+to the interval boundary (0 if the variant is located inside the
-distance to the nearest interval.
+interval; this is always true without --border).  They can be excluded
-* When --pfilter is present, high p-values are filtered out.
+with the 'minimal' modifier.
+* the 'distance' modifier adds 'DIST' and 'SGN' columns describing signed
---clump [PLINK report filename(s)...]
+distance to the nearest interval.
-Process association analysis report(s) with 'SNP' and p-value columns,
+* When --pfilter is present, high p-values are filtered out.
-organizing results by LD-based clumps.  Multiple filenames can be separated
-by spaces or commas.
+--clump [PLINK report filename(s)...]
+Process association analysis report(s) with 'SNP' and p-value columns,
---gene-report [PLINK report] [gene range file]
+organizing results by LD-based clumps.  Multiple filenames can be separated
-Generate a gene-based report from a variant-based report.
+by spaces or commas.
-* When --pfilter is present, high p-values are filtered out.
-* When --extract (without 'range') is present, only variants named in the
+--gene-report [PLINK report] [gene range file]
---extract file are considered.
+Generate a gene-based report from a variant-based report.
+* When --pfilter is present, high p-values are filtered out.
---meta-analysis [PLINK report filenames...]
+* When --extract (without 'range') is present, only variants named in the
---meta-analysis [PLINK report filenames...] + <logscale | qt>
+--extract file are considered.
-<no-map | no-allele> <study> <report-all> <weighted-z>
-Perform a meta-analysis on several variant-based reports with 'SNP' and
+--meta-analysis [PLINK report filenames...]
-'SE' fields.
+--meta-analysis [PLINK report filenames...] + <logscale | qt>
-* Normally, an 'OR' odds ratio field must also be present in each input
+<no-map | no-allele> <study> <report-all> <weighted-z>
-file.  With 'logscale', 'BETA' log-odds values/regression coefficients
+Perform a meta-analysis on several variant-based reports with 'SNP' and
-are expected instead, but the generated report will still contain odds
+'SE' fields.
-ratio estimates.  With 'qt', both input and output values are regression
+* Normally, an 'OR' odds ratio field must also be present in each input
-betas.
+file.  With 'logscale', 'BETA' log-odds values/regression coefficients
-* 'CHR', 'BP', and 'A1' fields are also normally required.  'no-map' causes
+are expected instead, but the generated report will still contain odds
-them to all be ignored, while 'no-allele' causes just 'A1' to be ignored.
+ratio estimates.  With 'qt', both input and output values are regression
-* If 'A2' fields are present, and neither 'no-map' nor 'no-allele' was
+betas.
-specified, A1/A2 allele flips are handled properly.  Otherwise, A1
+* 'CHR', 'BP', and 'A1' fields are also normally required.  'no-map' causes
-mismatches are thrown out.
+them to all be ignored, while 'no-allele' causes just 'A1' to be ignored.
-* 'study' causes study-specific effect estimates to be collated in the
+* If 'A2' fields are present, and neither 'no-map' nor 'no-allele' was
-meta-analysis report.
+specified, A1/A2 allele flips are handled properly.  Otherwise, A1
-* 'report-all' causes variants present in only a single input file to be
+mismatches are thrown out.
-included in the meta-analysis report.
+* 'study' causes study-specific effect estimates to be collated in the
-* 'weighted-z' requests weighted Z-score-based p-values (as computed by the
+meta-analysis report.
-Abecasis Lab's METAL software) in addition to the usual inverse
+* 'report-all' causes variants present in only a single input file to be
-variance-based analysis.  This requires P and effective sample size
+included in the meta-analysis report.
-fields.
+* 'weighted-z' requests weighted Z-score-based p-values (as computed by the
-* When --extract (without 'range') is present, only variants named in the
+Abecasis Lab's METAL software) in addition to the usual inverse
---extract file are considered.
+variance-based analysis.  This requires P and effective sample size
-* Unless 'no-map' is specified, chromosome filters are also respected.
+fields.
+* When --extract (without 'range') is present, only variants named in the
---fast-epistasis <boost | joint-effects | no-ueki> <case-only>
+--extract file are considered.
-<set-by-set | set-by-all> <nop>
+* Unless 'no-map' is specified, chromosome filters are also respected.
---epistasis <set-by-set | set-by-all>
-Scan for epistatic interactions.  --fast-epistasis inspects 3x3 joint
+--fast-epistasis <boost | joint-effects | no-ueki> <case-only>
-genotype count tables and only applies to case/control phenotypes, while
+<set-by-set | set-by-all> <nop>
---epistasis performs linear or logistic regression.
+--epistasis <set-by-set | set-by-all>
-* By default, --fast-epistasis uses the PLINK 1.07 allele-based test.  Two
+Scan for epistatic interactions.  --fast-epistasis inspects 3x3 joint
-newer tests are now supported: 'boost' invokes the likelihood ratio test
+genotype count tables and only applies to case/control phenotypes, while
-introduced by Wan X et al. (2010) BOOST: A Fast Approach to Detecting
+--epistasis performs linear or logistic regression.
-Gene-Gene Interactions in Genome-wide Case-Control Studies, while
+* By default, --fast-epistasis uses the PLINK 1.07 allele-based test.  Two
-'joint-effects' applies the joint effects test introduced in Ueki M,
+newer tests are now supported: 'boost' invokes the likelihood ratio test
-Cordell HJ (2012) Improved statistics for genome-wide interaction
+introduced by Wan X et al. (2010) BOOST: A Fast Approach to Detecting
-analysis.
+Gene-Gene Interactions in Genome-wide Case-Control Studies, while
-* The original --fast-epistasis test normally applies the variance and
+'joint-effects' applies the joint effects test introduced in Ueki M,
-empty cell corrections suggested by Ueki and Cordell's paper.  To disable
+Cordell HJ (2012) Improved statistics for genome-wide interaction
-them, use the 'no-ueki' modifier.
+analysis.
-* 'case-only' requests a case-only instead of a case/control test.
+* The original --fast-epistasis test normally applies the variance and
-* By default, all pairs of variants across the entire genome are tested.
+empty cell corrections suggested by Ueki and Cordell's paper.  To disable
-To just test pairs of variants within a single set, add the 'set-by-set'
+them, use the 'no-ueki' modifier.
-modifier and load exactly one set with --set/--make-set; with exactly two
+* 'case-only' requests a case-only instead of a case/control test.
-sets loaded, all variants in one set are tested against all variants in
+* By default, all pairs of variants across the entire genome are tested.
-the other.  'set-by-all' tests all variants in one set against the entire
+To just test pairs of variants within a single set, add the 'set-by-set'
-genome instead.
+modifier and load exactly one set with --set/--make-set; with exactly two
-* 'nop' strips p-values from the main report.
+sets loaded, all variants in one set are tested against all variants in
-* These computations can be subdivided with --parallel; however...
+the other.  'set-by-all' tests all variants in one set against the entire
---epistasis-summary-merge [common file prefix] [ct]
+genome instead.
-When a --{fast-}epistasis job is subdivided with --parallel, the main
+* 'nop' strips p-values from the main report.
-report can be assembled at the end by applying Unix 'cat' in the usual
+* These computations can be subdivided with --parallel; however...
-manner, but the .summary.1, .summary.2, ... files may require a specialized
+--epistasis-summary-merge [common file prefix] [ct]
-merge.  --epistasis-summary-merge takes care of the latter.
+When a --{fast-}epistasis job is subdivided with --parallel, the main
+report can be assembled at the end by applying Unix 'cat' in the usual
---twolocus [variant ID] [variant ID]
+manner, but the .summary.1, .summary.2, ... files may require a specialized
-Two-locus joint genotype count report.
+merge.  --epistasis-summary-merge takes care of the latter.
---score [filename] {i} {j} {k} <header> <sum | no-sum>
+--twolocus [variant ID] [variant ID]
-<no-mean-imputation | center> <include-cnt> <double-dosage>
+Two-locus joint genotype count report.
-Apply a linear scoring system to each sample.
-The input file should have one line per scored variant.  Variant IDs are
+--score [filename] {i} {j} {k} <header> <sum | no-sum>
-read from column #i, allele codes are read from column #j, and scores are
+<no-mean-imputation | center> <include-cnt> <double-dosage>
-read from column #k, where i defaults to 1, j defaults to i+1, and k
+Apply a linear scoring system to each sample.
-defaults to j+1.
+The input file should have one line per scored variant.  Variant IDs are
-* The 'header' modifier causes the first nonempty line of the input file to
+read from column #i, allele codes are read from column #j, and scores are
-be ignored; otherwise, --score assumes there is no header line.
+read from column #k, where i defaults to 1, j defaults to i+1, and k
-* By default, final scores are averages of the valid per-variant scores.
+defaults to j+1.
-The 'sum' modifier causes sums to be reported instead.  (This cannot be
+* The 'header' modifier causes the first nonempty line of the input file to
-used with 'no-mean-imputation'.  And for backward compatibility, 'sum' is
+be ignored; otherwise, --score assumes there is no header line.
-automatically on with dosage data unless 'no-sum' is specified.)
+* By default, final scores are averages of the valid per-variant scores.
-* By default, copies of the unnamed allele contribute zero to score, while
+The 'sum' modifier causes sums to be reported instead.  (This cannot be
-missing genotypes contribute an amount proportional to the loaded (via
+used with 'no-mean-imputation'.  And for backward compatibility, 'sum' is
---read-freq) or imputed allele frequency.  To throw out missing
+automatically on with dosage data unless 'no-sum' is specified.)
-observations instead (decreasing the denominator in the final average
+* By default, copies of the unnamed allele contribute zero to score, while
-when this happens), use the 'no-mean-imputation' modifier.
+missing genotypes contribute an amount proportional to the loaded (via
-* Alternatively, you can use the 'center' modifier to shift all scores to
+--read-freq) or imputed allele frequency.  To throw out missing
-mean zero.
+observations instead (decreasing the denominator in the final average
-* This command can be used with dosage data.  By default, the 'CNT' column
+when this happens), use the 'no-mean-imputation' modifier.
-is omitted from the output file in this case; use 'include-cnt' to keep
+* Alternatively, you can use the 'center' modifier to shift all scores to
-it.  Also, note that scores are multiplied by 0..1 dosages, not 0..2
+mean zero.
-diploid allele counts, unless the 'double-dosage' modifier is present.
+* This command can be used with dosage data.  By default, the 'CNT' column
+is omitted from the output file in this case; use 'include-cnt' to keep
---write-var-ranges [block ct]
+it.  Also, note that scores are multiplied by 0..1 dosages, not 0..2
-Divide the set of variants into equal-size blocks.  (Can be used with
+diploid allele counts, unless the 'double-dosage' modifier is present.
---snps to split a job across multiple machines.)
+--write-var-ranges [block ct]
-The following other flags are supported.  (Order of operations is described at
+Divide the set of variants into equal-size blocks.  (Can be used with
-https://www.cog-genomics.org/plink2/order .)
+--snps to split a job across multiple machines.)
---script [fname] : Include command-line options from file.
---rerun {log}    : Rerun commands in log (default 'plink.log').
+The following other flags are supported.  (Order of operations is described at
---version        : Display only version number before exiting.
+https://www.cog-genomics.org/plink2/order .)
---silent         : Suppress output to console.
+--script [fname] : Include command-line options from file.
---gplink         : Reserved for interoperation with gPLINK.
+--rerun {log}    : Rerun commands in log (default 'plink.log').
---missing-genotype [char] : Set missing genotype code (normally '0').
+--version        : Display only version number before exiting.
---double-id          : Set both FIDs and IIDs to the VCF/BCF sample ID.
+--silent         : Suppress output to console.
---const-fid {ID}     : Set all FIDs to the given constant (default '0').
+--gplink         : Reserved for interoperation with gPLINK.
---id-delim {d}       : Parse sample IDs as [FID][d][IID] (default delim '_').
+--missing-genotype [char] : Set missing genotype code (normally '0').
---vcf-idspace-to [c] : Convert spaces in sample IDs to the given character.
+--double-id          : Set both FIDs and IIDs to the VCF/BCF sample ID.
---biallelic-only <strict> <list> : Skip VCF variants with 2+ alt. alleles.
+--const-fid {ID}     : Set all FIDs to the given constant (default '0').
---vcf-min-qual [val]             : Skip VCF variants with low/missing QUAL.
+--id-delim {d}       : Parse sample IDs as [FID][d][IID] (default delim '_').
---vcf-filter {exception(s)...}   : Skip variants which have FILTER failures.
+--vcf-idspace-to [c] : Convert spaces in sample IDs to the given character.
---vcf-require-gt                 : Skip variants with no GT field.
+--biallelic-only <strict> <list> : Skip VCF variants with 2+ alt. alleles.
---vcf-min-gq [val]               : No-call a genotype when GQ is below the
+--vcf-min-qual [val]             : Skip VCF variants with low/missing QUAL.
-given threshold.
+--vcf-filter {exception(s)...}   : Skip variants which have FILTER failures.
---vcf-min-gp [val]               : No-call a genotype when 0-1 scaled GP is
+--vcf-require-gt                 : Skip variants with no GT field.
-below the given threshold.
+--vcf-min-gq [val]               : No-call a genotype when GQ is below the
---vcf-half-call [m]  : Specify how '0/.' and similar VCF GT values should be
+given threshold.
-handled.  The following four modes are supported:
+--vcf-min-gp [val]               : No-call a genotype when 0-1 scaled GP is
-* 'error'/'e' (default) errors out and reports line #.
+below the given threshold.
-* 'haploid'/'h' treats them as haploid calls.
+--vcf-half-call [m]  : Specify how '0/.' and similar VCF GT values should be
-* 'missing'/'m' treats them as missing.
+handled.  The following four modes are supported:
-* 'reference'/'r' treats the missing value as 0.
+* 'error'/'e' (default) errors out and reports line #.
---oxford-single-chr [chr nm] : Specify single-chromosome .gen file with
+* 'haploid'/'h' treats them as haploid calls.
-ignorable first column.
+* 'missing'/'m' treats them as missing.
---oxford-pheno-name [col nm] : Import named phenotype from the .sample file.
+* 'reference'/'r' treats the missing value as 0.
---hard-call-threshold [val]  : When an Oxford-format fileset is loaded, calls
+--oxford-single-chr [chr nm] : Specify single-chromosome .gen file with
---hard-call-threshold random   with uncertainty level greater than 0.1 are
+ignorable first column.
-normally treated as missing.  You can adjust
+--oxford-pheno-name [col nm] : Import named phenotype from the .sample file.
-this threshold by providing a numeric
+--hard-call-threshold [val]  : When an Oxford-format fileset is loaded, calls
-parameter, or randomize all calls with
+--hard-call-threshold random   with uncertainty level greater than 0.1 are
-'random'.
+normally treated as missing.  You can adjust
---missing-code {string list} : Comma-delimited list of missing phenotype
+this threshold by providing a numeric
-(alias: --missing_code)      values for Oxford-format filesets (def. 'NA').
+parameter, or randomize all calls with
---simulate-ncases [num]   : Set --simulate case count (default 1000).
+'random'.
---simulate-ncontrols [n]  : Set --simulate control count (default 1000).
+--missing-code {string list} : Comma-delimited list of missing phenotype
---simulate-prevalence [p] : Set --simulate disease prevalence (default 0.01).
+(alias: --missing_code)      values for Oxford-format filesets (def. 'NA').
---simulate-n [num]        : Set --simulate-qt sample count (default 1000).
+--simulate-ncases [num]   : Set --simulate case count (default 1000).
---simulate-label [prefix] : Set --simulate{-qt} FID/IID name prefix.
+--simulate-ncontrols [n]  : Set --simulate control count (default 1000).
---simulate-missing [freq] : Set --simulate{-qt} missing genotype frequency.
+--simulate-prevalence [p] : Set --simulate disease prevalence (default 0.01).
---allow-extra-chr <0>     : Permit unrecognized chromosome codes.  The '0'
+--simulate-n [num]        : Set --simulate-qt sample count (default 1000).
-(alias: --aec)            modifier causes them to be treated as if they had
+--simulate-label [prefix] : Set --simulate{-qt} FID/IID name prefix.
-been set to zero.
+--simulate-missing [freq] : Set --simulate{-qt} missing genotype frequency.
---chr-set [autosome ct] <no-x> <no-y> <no-xy> <no-mt> :
+--allow-extra-chr <0>     : Permit unrecognized chromosome codes.  The '0'
-Specify a nonhuman chromosome set.  The first parameter sets the number of
+(alias: --aec)            modifier causes them to be treated as if they had
-diploid autosome pairs if positive, or haploid chromosomes if negative.
+been set to zero.
-Given diploid autosomes, the remaining modifiers indicate the absence of
+--chr-set [autosome ct] <no-x> <no-y> <no-xy> <no-mt> :
-the named non-autosomal chromosomes.
+Specify a nonhuman chromosome set.  The first parameter sets the number of
---cow/--dog/--horse/--mouse/--rice/--sheep : Shortcuts for those species.
+diploid autosome pairs if positive, or haploid chromosomes if negative.
---autosome-num [value]    : Alias for '--chr-set [value] no-y no-xy no-mt'.
+Given diploid autosomes, the remaining modifiers indicate the absence of
---cm-map [fname pattern] {chr} : Use SHAPEIT-format recombination maps to set
+the named non-autosomal chromosomes.
-centimorgan positions.  To process more than
+--cow/--dog/--horse/--mouse/--rice/--sheep : Shortcuts for those species.
-one chromosome, include a '@' in the first
+--autosome-num [value]    : Alias for '--chr-set [value] no-y no-xy no-mt'.
-parameter where the chrom. number belongs,
+--cm-map [fname pattern] {chr} : Use SHAPEIT-format recombination maps to set
-e.g. 'genetic_map_chr@_combined_b37.txt'.
+centimorgan positions.  To process more than
---zero-cms         : Zero out centimorgan positions.
+one chromosome, include a '@' in the first
---pheno [fname]  : Load phenotype data from the specified file, instead of
+parameter where the chrom. number belongs,
-using the values in the main input fileset.
+e.g. 'genetic_map_chr@_combined_b37.txt'.
---all-pheno      : For basic association tests, loop through all phenotypes
+--zero-cms         : Zero out centimorgan positions.
-in --pheno file.
+--pheno [fname]  : Load phenotype data from the specified file, instead of
---mpheno [n]     : Load phenotype from column (n+2) in --pheno file.
+using the values in the main input fileset.
---pheno-name [c] : If --pheno file has a header row, use column with the
+--all-pheno      : For basic association tests, loop through all phenotypes
-given name.
+in --pheno file.
---pheno-merge    : When the main input fileset contains an phenotype value
+--mpheno [n]     : Load phenotype from column (n+2) in --pheno file.
-for a sample, but the --pheno file does not, use the
+--pheno-name [c] : If --pheno file has a header row, use column with the
-original value instead of treating the phenotype as
+given name.
-missing.
+--pheno-merge    : When the main input fileset contains an phenotype value
---missing-phenotype [v] : Set missing phenotype value (normally -9).
+for a sample, but the --pheno file does not, use the
---1                     : Expect case/control phenotypes to be coded as
+original value instead of treating the phenotype as
-0 = control, 1 = case, instead of the usual
+missing.
-0 = missing, 1 = control, 2 = case.
+--missing-phenotype [v] : Set missing phenotype value (normally -9).
---make-pheno [fn] [val] : Define a new case/control phenotype.  If the val
+--1                     : Expect case/control phenotypes to be coded as
-parameter is '*', all samples listed in the given
+0 = control, 1 = case, instead of the usual
-file are cases, and everyone else is a control.
+0 = missing, 1 = control, 2 = case.
-(Note that, in some shells, it is necessary to
+--make-pheno [fn] [val] : Define a new case/control phenotype.  If the val
-surround the * with quotes.)
+parameter is '*', all samples listed in the given
-Otherwise, all samples with third column entry
+file are cases, and everyone else is a control.
-equal to the val parameter are cases, and all other
+(Note that, in some shells, it is necessary to
-samples mentioned in the file are controls.
+surround the * with quotes.)
---tail-pheno [Lt] {Hbt} : Downcode a scalar phenotype to a case/control
+Otherwise, all samples with third column entry
-phenotype.  All samples with phenotype values
+equal to the val parameter are cases, and all other
-greater than Hbt are cases, and all with values
+samples mentioned in the file are controls.
-less than or equal to Lt are controls.  If Hbt is
+--tail-pheno [Lt] {Hbt} : Downcode a scalar phenotype to a case/control
-unspecified, it is equal to Lt; otherwise,
+phenotype.  All samples with phenotype values
-in-between phenotype values are set to missing.
+greater than Hbt are cases, and all with values
---covar [filename] <keep-pheno-on-missing-cov> : Specify covariate file.
+less than or equal to Lt are controls.  If Hbt is
---covar-name [...]      : Specify covariate(s) in --covar file by name.
+unspecified, it is equal to Lt; otherwise,
-Separate multiple names with spaces or commas, and
+in-between phenotype values are set to missing.
-use dashes to designate ranges.
+--covar [filename] <keep-pheno-on-missing-cov> : Specify covariate file.
---covar-number [...]    : Specify covariate(s) in --covar file by index.
+--covar-name [...]      : Specify covariate(s) in --covar file by name.
---no-const-covar        : Exclude constant covariates.
+Separate multiple names with spaces or commas, and
---within [f] <keep-NA>  : Specify initial cluster assignments.
+use dashes to designate ranges.
---mwithin [n]           : Load cluster assignments from column n+2.
+--covar-number [...]    : Specify covariate(s) in --covar file by index.
---family                : Create a cluster for each family ID.
+--no-const-covar        : Exclude constant covariates.
---loop-assoc [f] <keep-NA>    : Run specified case/control association
+--within [f] <keep-NA>  : Specify initial cluster assignments.
-commands once for each cluster in the file,
+--mwithin [n]           : Load cluster assignments from column n+2.
-using cluster membership as the phenotype.
+--family                : Create a cluster for each family ID.
---set [filename]              : Load sets from a .set file.
+--loop-assoc [f] <keep-NA>    : Run specified case/control association
---set-names [name(s)...]      : Load only sets named on the command line.
+commands once for each cluster in the file,
-Use spaces to separate multiple names.
+using cluster membership as the phenotype.
---subset [filename]           : Load only sets named in the given text file.
+--set [filename]              : Load sets from a .set file.
---set-collapse-all [set name] : Merge all sets.
+--set-names [name(s)...]      : Load only sets named on the command line.
---complement-sets             : Invert all sets.  (Names gain 'C_' prefixes.)
+Use spaces to separate multiple names.
---make-set-complement-all [s] : --set-collapse-all + inversion.
+--subset [filename]           : Load only sets named in the given text file.
---make-set [filename]         : Define sets from a list of named bp ranges.
+--set-collapse-all [set name] : Merge all sets.
---make-set-border [kbs]       : Stretch regions in --make-set file.
+--complement-sets             : Invert all sets.  (Names gain 'C_' prefixes.)
---make-set-collapse-group     : Define sets from groups instead of sets in
+--make-set-complement-all [s] : --set-collapse-all + inversion.
---make-set file.
+--make-set [filename]         : Define sets from a list of named bp ranges.
---keep [filename]     : Exclude all samples not named in the file.
+--make-set-border [kbs]       : Stretch regions in --make-set file.
---remove [filename]   : Exclude all samples named in the file.
+--make-set-collapse-group     : Define sets from groups instead of sets in
---keep-fam [filename] : Exclude all families not named in the file.
+--make-set file.
---remove-fam [fname]  : Exclude all families named in the file.
+--keep [filename]     : Exclude all samples not named in the file.
---extract <range> [f] : Exclude all variants not named in the file.
+--remove [filename]   : Exclude all samples named in the file.
---exclude <range> [f] : Exclude all variants named in the file.
+--keep-fam [filename] : Exclude all families not named in the file.
---keep-clusters [filename]          : These can be used individually or in
+--remove-fam [fname]  : Exclude all families named in the file.
---keep-cluster-names [name(s)...]     combination to define a list of
+--extract <range> [f] : Exclude all variants not named in the file.
-clusters to keep; all samples not in a
+--exclude <range> [f] : Exclude all variants named in the file.
-cluster in that list are then excluded.
+--keep-clusters [filename]          : These can be used individually or in
-Use spaces to separate cluster names
+--keep-cluster-names [name(s)...]     combination to define a list of
-for --keep-cluster-names.
+clusters to keep; all samples not in a
---remove-clusters [filename]        : Exclude all clusters named in the file.
+cluster in that list are then excluded.
---remove-cluster-names [name(s)...] : Exclude the named clusters.
+Use spaces to separate cluster names
---gene [sets...] : Exclude variants not in a set named on the command line.
+for --keep-cluster-names.
-(Separate multiple set names with spaces.)
+--remove-clusters [filename]        : Exclude all clusters named in the file.
---gene-all       : Exclude variants which aren't a member of any set.  (PLINK
+--remove-cluster-names [name(s)...] : Exclude the named clusters.
-1.07 automatically did this under some circumstances.)
+--gene [sets...] : Exclude variants not in a set named on the command line.
---attrib [f] {att lst} : Given a file assigning attributes to variants, and a
+(Separate multiple set names with spaces.)
---attrib-indiv [f] {a}   comma-delimited list (with no whitespace) of
+--gene-all       : Exclude variants which aren't a member of any set.  (PLINK
-attribute names, remove variants/samples which are
+1.07 automatically did this under some circumstances.)
-either missing from the file or don't have any of
+--attrib [f] {att lst} : Given a file assigning attributes to variants, and a
-the listed attributes.  If some attribute names in
+--attrib-indiv [f] {a}   comma-delimited list (with no whitespace) of
-the list are preceded by '-', they are treated as
+attribute names, remove variants/samples which are
-'negative match conditions' instead: variants with
+either missing from the file or don't have any of
-at least one negative match attribute are removed.
+the listed attributes.  If some attribute names in
-The first character in the list cannot be a '-', due
+the list are preceded by '-', they are treated as
-to how command-line parsing works; add a comma in
+'negative match conditions' instead: variants with
-front to get around this.
+at least one negative match attribute are removed.
---chr [chrs...]  : Exclude all variants not on the given chromosome(s).
+The first character in the list cannot be a '-', due
-Valid choices for humans are 0 (unplaced), 1-22, X, Y, XY,
+to how command-line parsing works; add a comma in
-and MT.  Separate multiple chromosomes with spaces and/or
+front to get around this.
-commas, and use a dash (no adjacent spaces permitted) to
+--chr [chrs...]  : Exclude all variants not on the given chromosome(s).
-denote a range, e.g. '--chr 1-4, 22, xy'.
+Valid choices for humans are 0 (unplaced), 1-22, X, Y, XY,
---not-chr [...]  : Reverse of --chr (exclude variants on listed chromosomes).
+and MT.  Separate multiple chromosomes with spaces and/or
---autosome       : Exclude all non-autosomal variants.
+commas, and use a dash (no adjacent spaces permitted) to
---autosome-xy    : Exclude all non-autosomal variants, except those with
+denote a range, e.g. '--chr 1-4, 22, xy'.
-chromosome code XY (pseudo-autosomal region of X).
+--not-chr [...]  : Reverse of --chr (exclude variants on listed chromosomes).
---snps-only <just-acgt> : Exclude non-SNP variants.  By default, SNP = both
+--autosome       : Exclude all non-autosomal variants.
-allele codes are single-character; 'just-acgt'
+--autosome-xy    : Exclude all non-autosomal variants, except those with
-restricts SNP codes to {A,C,G,T,a,c,g,t,[missing]}.
+chromosome code XY (pseudo-autosomal region of X).
---from [var ID]  : Use ID(s) to specify a variant range to load.  When used
+--snps-only <just-acgt> : Exclude non-SNP variants.  By default, SNP = both
---to   [var ID]    together, both variants must be on the same chromosome.
+allele codes are single-character; 'just-acgt'
---snp  [var ID]  : Specify a single variant to load.
+restricts SNP codes to {A,C,G,T,a,c,g,t,[missing]}.
---exclude-snp [] : Specify a single variant to exclude.
+--from [var ID]  : Use ID(s) to specify a variant range to load.  When used
---window  [kbs]  : With --snp or --exclude-snp, loads/excludes all variants
+--to   [var ID]    together, both variants must be on the same chromosome.
-within half the specified kb distance of the named one.
+--snp  [var ID]  : Specify a single variant to load.
---from-bp [pos]  : Use physical position(s) to define a variant range to
+--exclude-snp [] : Specify a single variant to exclude.
---to-bp   [pos]    load.  --from-kb/--to-kb/--from-mb/--to-mb allow decimal
+--window  [kbs]  : With --snp or --exclude-snp, loads/excludes all variants
---from-kb [pos]    values.  You must also specify a single chromosome (using
+within half the specified kb distance of the named one.
---to-kb   [pos]    e.g. --chr) when using these flags.
+--from-bp [pos]  : Use physical position(s) to define a variant range to
---from-mb [pos]
+--to-bp   [pos]    load.  --from-kb/--to-kb/--from-mb/--to-mb allow decimal
---to-mb   [pos]
+--from-kb [pos]    values.  You must also specify a single chromosome (using
---snps [var IDs...]  : Use IDs to specify variant range(s) to load or
+--to-kb   [pos]    e.g. --chr) when using these flags.
---exclude-snps [...]   exclude.  E.g. '--snps rs1111-rs2222, rs3333, rs4444'.
+--from-mb [pos]
---thin [p]       : Randomly remove variants, retaining each with prob. p.
+--to-mb   [pos]
---thin-count [n] : Randomly remove variants until n of them remain.
+--snps [var IDs...]  : Use IDs to specify variant range(s) to load or
---bp-space [bps] : Remove variants so that each pair is no closer than the
+--exclude-snps [...]   exclude.  E.g. '--snps rs1111-rs2222, rs3333, rs4444'.
-given bp distance.  (Equivalent to VCFtools --thin.)
+--thin [p]       : Randomly remove variants, retaining each with prob. p.
---thin-indiv [p]         : Randomly remove samples, retaining with prob. p.
+--thin-count [n] : Randomly remove variants until n of them remain.
---thin-indiv-count [n]   : Randomly remove samples until n of them remain.
+--bp-space [bps] : Remove variants so that each pair is no closer than the
---filter [f] [val(s)...] : Exclude all samples without a 3rd column entry in
+given bp distance.  (Equivalent to VCFtools --thin.)
-the given file matching one of the given
+--thin-indiv [p]         : Randomly remove samples, retaining with prob. p.
-space-separated value(s).
+--thin-indiv-count [n]   : Randomly remove samples until n of them remain.
---mfilter [n]            : Match against (n+2)th column instead.
+--filter [f] [val(s)...] : Exclude all samples without a 3rd column entry in
---geno {val}     : Exclude variants with missing call frequencies greater
+the given file matching one of the given
-than a threshold (default 0.1).  (Note that the default
+space-separated value(s).
-threshold is only applied if --geno is invoked without a
+--mfilter [n]            : Match against (n+2)th column instead.
-parameter; when --geno is not invoked, no per-variant
+--geno {val}     : Exclude variants with missing call frequencies greater
-missing call frequency ceiling is enforced at all.  Other
+than a threshold (default 0.1).  (Note that the default
-inclusion/exclusion default thresholds work the same way.)
+threshold is only applied if --geno is invoked without a
---mind {val}     : Exclude samples with missing call frequencies greater than
+parameter; when --geno is not invoked, no per-variant
-a threshold (default 0.1).
+missing call frequency ceiling is enforced at all.  Other
---oblig-missing [f1] [f2] : Specify blocks of missing genotype calls for
+inclusion/exclusion default thresholds work the same way.)
---geno/--mind to ignore.  The first file should
+--mind {val}     : Exclude samples with missing call frequencies greater than
-have variant IDs in the first column and block
+a threshold (default 0.1).
-IDs in the second, while the second file should
+--oblig-missing [f1] [f2] : Specify blocks of missing genotype calls for
-have FIDs in the first column, IIDs in the
+--geno/--mind to ignore.  The first file should
-second, and block IDs in the third.
+have variant IDs in the first column and block
---prune             : Remove samples with missing phenotypes.
+IDs in the second, while the second file should
---maf {freq}        : Exclude variants with minor allele frequency lower than
+have FIDs in the first column, IIDs in the
-a threshold (default 0.01).
+second, and block IDs in the third.
---max-maf [freq]    : Exclude variants with MAF greater than the threshold.
+--prune             : Remove samples with missing phenotypes.
---mac [ct]          : Exclude variants with minor allele count lower than the
+--maf {freq}        : Exclude variants with minor allele frequency lower than
-(alias: --min-ac)   given threshold.
+a threshold (default 0.01).
---max-mac [ct]      : Exclude variants with minor allele count greater than
+--max-maf [freq]    : Exclude variants with MAF greater than the threshold.
-(alias: --max-ac)   the given threshold.
+--mac [ct]          : Exclude variants with minor allele count lower than the
---maf-succ       : Rule of succession MAF estimation (used in EIGENSOFT).
+(alias: --min-ac)   given threshold.
-Given j observations of one allele and k >= j observations
+--max-mac [ct]      : Exclude variants with minor allele count greater than
-of the other, infer a MAF of (j+1) / (j+k+2), rather than
+(alias: --max-ac)   the given threshold.
-the default j / (j+k).
+--maf-succ       : Rule of succession MAF estimation (used in EIGENSOFT).
---read-freq [fn] : Estimate MAFs and heterozygote frequencies from the given
+Given j observations of one allele and k >= j observations
---freq{x} report, instead of the input fileset.
+of the other, infer a MAF of (j+1) / (j+k+2), rather than
---hwe [p] <midp> <include-nonctrl> : Exclude variants with Hardy-Weinberg
+the default j / (j+k).
-equilibrium exact test p-values below a
+--read-freq [fn] : Estimate MAFs and heterozygote frequencies from the given
-threshold.
+--freq{x} report, instead of the input fileset.
---me [t] [v] <var-first> : Filter out trios and variants with Mendel error
+--hwe [p] <midp> <include-nonctrl> : Exclude variants with Hardy-Weinberg
-rates exceeding the given thresholds.
+equilibrium exact test p-values below a
---me-exclude-one {ratio} : Make --me exclude only one sample per trio.
+threshold.
---qual-scores [f] {qcol} {IDcol} {skip} : Filter out variants with
+--me [t] [v] <var-first> : Filter out trios and variants with Mendel error
-out-of-range quality scores.
+rates exceeding the given thresholds.
-Default range is now [0, \infty ).
+--me-exclude-one {ratio} : Make --me exclude only one sample per trio.
---qual-threshold [min qual score]       : Set --qual-scores range floor.
+--qual-scores [f] {qcol} {IDcol} {skip} : Filter out variants with
---qual-max-threshold [max qual score]   : Set --qual-scores range ceiling.
+out-of-range quality scores.
---allow-no-sex   : Do not treat ambiguous-sex samples as having missing
+Default range is now [0, \infty ).
-phenotypes in analysis commands.  (Automatic /w --no-sex.)
+--qual-threshold [min qual score]       : Set --qual-scores range floor.
---must-have-sex  : Force ambiguous-sex phenotypes to missing on
+--qual-max-threshold [max qual score]   : Set --qual-scores range ceiling.
---make-bed/--make-just-fam/--recode/--write-covar.
+--allow-no-sex   : Do not treat ambiguous-sex samples as having missing
---filter-cases       : Include only cases in the current analysis.
+phenotypes in analysis commands.  (Automatic /w --no-sex.)
---filter-controls    : Include only controls.
+--must-have-sex  : Force ambiguous-sex phenotypes to missing on
---filter-males       : Include only males.
+--make-bed/--make-just-fam/--recode/--write-covar.
---filter-females     : Include only females.
+--filter-cases       : Include only cases in the current analysis.
---filter-founders    : Include only founders.
+--filter-controls    : Include only controls.
---filter-nonfounders : Include only nonfounders.
+--filter-males       : Include only males.
---nonfounders        : Include nonfounders in allele freq/HWE calculations.
+--filter-females     : Include only females.
---make-founders <require-2-missing> <first> : Clear parental IDs for those
+--filter-founders    : Include only founders.
-with 1+ missing parent(s).
+--filter-nonfounders : Include only nonfounders.
---recode-allele [fn] : With --recode A/A-transpose/AD, count alleles named in
+--nonfounders        : Include nonfounders in allele freq/HWE calculations.
-the file (otherwise A1 alleles are always counted).
+--make-founders <require-2-missing> <first> : Clear parental IDs for those
---output-chr [MT code] : Set chromosome coding scheme in output files by
+with 1+ missing parent(s).
-providing the desired human mitochondrial code.
+--recode-allele [fn] : With --recode A/A-transpose/AD, count alleles named in
-(Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM',
+the file (otherwise A1 alleles are always counted).
-and 'chrMT'.)
+--output-chr [MT code] : Set chromosome coding scheme in output files by
---output-missing-genotype [ch] : Set the code used to represent missing
+providing the desired human mitochondrial code.
-genotypes in output files (normally the
+(Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM',
---missing-genotype value).
+and 'chrMT'.)
---output-missing-phenotype [s] : Set the string used to represent missing
+--output-missing-genotype [ch] : Set the code used to represent missing
-phenotypes in output files (normally the
+genotypes in output files (normally the
---missing-phenotype value).
+--missing-genotype value).
---zero-cluster [f] : In combination with --within/--family, set blocks of
+--output-missing-phenotype [s] : Set the string used to represent missing
-genotype calls to missing.  The input file should have
+phenotypes in output files (normally the
-variant IDs in the first column and cluster IDs in the
+--missing-phenotype value).
-second.  This must now be used with --make-bed and no
+--zero-cluster [f] : In combination with --within/--family, set blocks of
-other output commands.
+genotype calls to missing.  The input file should have
---set-hh-missing       : Cause --make-bed and --recode to set heterozygous
+variant IDs in the first column and cluster IDs in the
-haploid genotypes to missing.
+second.  This must now be used with --make-bed and no
---set-mixed-mt-missing : Cause --make-bed and --recode to set mixed MT
+other output commands.
-genotypes to missing.
+--set-hh-missing       : Cause --make-bed and --recode to set heterozygous
---split-x [bp1] [bp2] <no-fail> : Changes chromosome code of all X chromosome
+haploid genotypes to missing.
---split-x [build] <no-fail>       variants with bp position <= bp1 or >= bp2
+--set-mixed-mt-missing : Cause --make-bed and --recode to set mixed MT
-to XY.  The following build codes are
+genotypes to missing.
-supported as shorthand:
+--split-x [bp1] [bp2] <no-fail> : Changes chromosome code of all X chromosome
-* 'b36'/'hg18' = NCBI 36, 2709521/154584237
+--split-x [build] <no-fail>       variants with bp position <= bp1 or >= bp2
-* 'b37'/'hg19' = GRCh37, 2699520/154931044
+to XY.  The following build codes are
-* 'b38'/'hg38' = GRCh38, 2781479/155701383
+supported as shorthand:
-By default, PLINK errors out when no
+* 'b36'/'hg18' = NCBI 36, 2709521/154584237
-variants would be affected by --split-x;
+* 'b37'/'hg19' = GRCh37, 2699520/154931044
-the 'no-fail' modifier (useful in scripts)
+* 'b38'/'hg38' = GRCh38, 2781479/155701383
-overrides this.
+By default, PLINK errors out when no
---merge-x <no-fail>             : Merge XY chromosome back with X.
+variants would be affected by --split-x;
---set-me-missing  : Cause --make-bed to set Mendel errors to missing.
+the 'no-fail' modifier (useful in scripts)
---fill-missing-a2 : Cause --make-bed to replace all missing calls with
+overrides this.
-homozygous A2 calls.
+--merge-x <no-fail>             : Merge XY chromosome back with X.
---set-missing-var-ids [t]   : Given a template string with a '@' where the
+--set-me-missing  : Cause --make-bed to set Mendel errors to missing.
-chromosome code should go and '#' where the bp
+--fill-missing-a2 : Cause --make-bed to replace all missing calls with
-coordinate belongs, --set-missing-var-ids
+homozygous A2 calls.
-assigns chromosome-and-bp-based IDs to unnamed
+--set-missing-var-ids [t]   : Given a template string with a '@' where the
-variants.
+chromosome code should go and '#' where the bp
-You may also use '$1' and '$2' to refer to
+coordinate belongs, --set-missing-var-ids
-allele names in the template string, and in
+assigns chromosome-and-bp-based IDs to unnamed
-fact this becomes essential when multiple
+variants.
-variants share the same coordinate.
+You may also use '$1' and '$2' to refer to
---new-id-max-allele-len [n] : Specify maximum number of leading characters
+allele names in the template string, and in
-from allele names to include in new variant IDs
+fact this becomes essential when multiple
-(default 23).
+variants share the same coordinate.
---missing-var-code [string] : Change unnamed variant code (default '.').
+--new-id-max-allele-len [n] : Specify maximum number of leading characters
---update-chr  [f] {chrcol} {IDcol}  {skip} : Update variant chromosome codes.
+from allele names to include in new variant IDs
---update-cm   [f] {cmcol}  {IDcol}  {skip} : Update centimorgan positions.
+(default 23).
---update-map  [f] {bpcol}  {IDcol}  {skip} : Update variant bp positions.
+--missing-var-code [string] : Change unnamed variant code (default '.').
---update-name [f] {newcol} {oldcol} {skip} : Update variant IDs.
+--update-chr  [f] {chrcol} {IDcol}  {skip} : Update variant chromosome codes.
---update-alleles [fname] : Update variant allele codes.
+--update-cm   [f] {cmcol}  {IDcol}  {skip} : Update centimorgan positions.
---allele1234 <multichar> : Interpret/recode A/C/G/T alleles as 1/2/3/4.
+--update-map  [f] {bpcol}  {IDcol}  {skip} : Update variant bp positions.
-With 'multichar', converts all A/C/G/Ts in allele
+--update-name [f] {newcol} {oldcol} {skip} : Update variant IDs.
-names to 1/2/3/4s.
+--update-alleles [fname] : Update variant allele codes.
---alleleACGT <multichar> : Reverse of --allele1234.
+--allele1234 <multichar> : Interpret/recode A/C/G/T alleles as 1/2/3/4.
---update-ids [f]     : Update sample IDs.
+With 'multichar', converts all A/C/G/Ts in allele
---update-parents [f] : Update parental IDs.
+names to 1/2/3/4s.
---update-sex [f] {n} : Update sexes.  Sex (1 or M = male, 2 or F = female, 0
+--alleleACGT <multichar> : Reverse of --allele1234.
-= missing) is loaded from column n+2 (default n is 1).
+--update-ids [f]     : Update sample IDs.
---flip [filename]    : Flip alleles (A<->T, C<->G) for SNP IDs in the file.
+--update-parents [f] : Update parental IDs.
---flip-subset [fn]   : Only apply --flip to samples in --flip-subset file.
+--update-sex [f] {n} : Update sexes.  Sex (1 or M = male, 2 or F = female, 0
---flip-scan-window [ct+1] : Set --flip-scan max variant ct dist. (def. 10).
+= missing) is loaded from column n+2 (default n is 1).
---flip-scan-window-kb [x] : Set --flip-scan max kb distance (default 1000).
+--flip [filename]    : Flip alleles (A<->T, C<->G) for SNP IDs in the file.
---flip-scan-threshold [x] : Set --flip-scan min correlation (default 0.5).
+--flip-subset [fn]   : Only apply --flip to samples in --flip-subset file.
---keep-allele-order  : Keep the allele order defined in the .bim file,
+--flip-scan-window [ct+1] : Set --flip-scan max variant ct dist. (def. 10).
---real-ref-alleles     instead of forcing A2 to be the major allele.
+--flip-scan-window-kb [x] : Set --flip-scan max kb distance (default 1000).
---real-ref-alleles also removes 'PR' from the INFO
+--flip-scan-threshold [x] : Set --flip-scan min correlation (default 0.5).
-values emitted by --recode vcf{-fid/-iid}.
+--keep-allele-order  : Keep the allele order defined in the .bim file,
---a1-allele [f] {a1col} {IDcol} {skip} : Force alleles in the file to A1.
+--real-ref-alleles     instead of forcing A2 to be the major allele.
---a2-allele [filename] {a2col} {IDcol} {skip} :
+--real-ref-alleles also removes 'PR' from the INFO
-Force alleles in the file to A2.  ("--a2-allele [VCF filename] 4 3 '#'",
+values emitted by --recode vcf{-fid/-iid}.
-which scrapes reference allele assignments from a VCF file, is especially
+--a1-allele [f] {a1col} {IDcol} {skip} : Force alleles in the file to A1.
-useful.)
+--a2-allele [filename] {a2col} {IDcol} {skip} :
---indiv-sort [m] {f} : Specify FID/IID sort order.  The following four modes
+Force alleles in the file to A2.  ("--a2-allele [VCF filename] 4 3 '#'",
-are supported:
+which scrapes reference allele assignments from a VCF file, is especially
-* 'none'/'0' keeps samples in the order they were
+useful.)
-loaded.  Default for non-merge operations.
+--indiv-sort [m] {f} : Specify FID/IID sort order.  The following four modes
-* 'natural'/'n' invokes 'natural sort', e.g.
+are supported:
-'id2' < 'ID3' < 'id10'.  Default when merging.
+* 'none'/'0' keeps samples in the order they were
-* 'ascii'/'a' sorts in ASCII order, e.g.
+loaded.  Default for non-merge operations.
-'ID3' < 'id10' < 'id2'.
+* 'natural'/'n' invokes 'natural sort', e.g.
-* 'file'/'f' uses the order in the given file (named
+'id2' < 'ID3' < 'id10'.  Default when merging.
-in the second parameter).
+* 'ascii'/'a' sorts in ASCII order, e.g.
-For now, only --merge/--bmerge/--merge-list and
+'ID3' < 'id10' < 'id2'.
---make-bed/--make-just-fam respect this flag.
+* 'file'/'f' uses the order in the given file (named
---with-phenotype <no-parents> <no-sex | female-2> : Include more sample info
+in the second parameter).
-in new .cov file.
+For now, only --merge/--bmerge/--merge-list and
---dummy-coding {N} <no-round> : Split categorical variables (n categories,
+--make-bed/--make-just-fam respect this flag.
-2 < n <= N, default N is 49) into n-1 binary
+--with-phenotype <no-parents> <no-sex | female-2> : Include more sample info
-dummy variables when writing covariate file.
+in new .cov file.
---merge-mode [n]   : Adjust --{b}merge/--merge-list behavior based on a
+--dummy-coding {N} <no-round> : Split categorical variables (n categories,
-numeric code.
+2 < n <= N, default N is 49) into n-1 binary
-1 (default) = ignore missing calls, otherwise difference
+dummy variables when writing covariate file.
--> missing
+--merge-mode [n]   : Adjust --{b}merge/--merge-list behavior based on a
-2 = only overwrite originally missing calls
+numeric code.
-3 = only overwrite when nonmissing in new file
+1 (default) = ignore missing calls, otherwise difference
-4/5 = never overwrite and always overwrite, respectively
+-> missing
-6 = report all mismatching calls without merging
+2 = only overwrite originally missing calls
-7 = report mismatching nonmissing calls without merging
+3 = only overwrite when nonmissing in new file
---merge-equal-pos  : With --merge/--bmerge/--merge-list, merge variants with
+4/5 = never overwrite and always overwrite, respectively
-different names but identical positions.  (Exception:
+6 = report all mismatching calls without merging
-same-position chromosome code 0 variants aren't merged.)
+7 = report mismatching nonmissing calls without merging
---mendel-duos      : Make Mendel error checks consider samples with only one
+--merge-equal-pos  : With --merge/--bmerge/--merge-list, merge variants with
-parent in the dataset.
+different names but identical positions.  (Exception:
---mendel-multigen  : Make Mendel error checks consider (great-)grandparental
+same-position chromosome code 0 variants aren't merged.)
-genotypes when parental genotype data is missing.
+--mendel-duos      : Make Mendel error checks consider samples with only one
---ld-window [ct+1] : Set --r/--r2 max variant ct pairwise distance (usu. 10).
+parent in the dataset.
---ld-window-kb [x] : Set --r/--r2 max kb pairwise distance (usually 1000).
+--mendel-multigen  : Make Mendel error checks consider (great-)grandparental
---ld-window-cm [x] : Set --r/--r2 max centimorgan pairwise distance.
+genotypes when parental genotype data is missing.
---ld-window-r2 [x] : Set threshold for --r2 report inclusion (usually 0.2).
+--ld-window [ct+1] : Set --r/--r2 max variant ct pairwise distance (usu. 10).
---ld-snp [var ID]  : Set first variant in all --r/--r2 pairs.
+--ld-window-kb [x] : Set --r/--r2 max kb pairwise distance (usually 1000).
---ld-snps [vID...] : Restrict first --r/--r2 variant to the given ranges.
+--ld-window-cm [x] : Set --r/--r2 max centimorgan pairwise distance.
---ld-snp-list [f]  : Restrict first --r/--r2 var. to those named in the file.
+--ld-window-r2 [x] : Set threshold for --r2 report inclusion (usually 0.2).
---list-all         : Generate the 'all' mode report when using --show-tags in
+--ld-snp [var ID]  : Set first variant in all --r/--r2 pairs.
-file mode.
+--ld-snps [vID...] : Restrict first --r/--r2 variant to the given ranges.
---tag-kb [kbs]     : Set --show-tags max tag kb distance (default 250).
+--ld-snp-list [f]  : Restrict first --r/--r2 var. to those named in the file.
---tag-r2 [val]     : Set --show-tags min tag r-squared (default 0.8)
+--list-all         : Generate the 'all' mode report when using --show-tags in
---tag-mode2        : Use two-column --show-tags (file mode) I/O format.
+file mode.
---ld-xchr [code]   : Set Xchr model for --indep{-pairwise}, --r/--r2,
+--tag-kb [kbs]     : Set --show-tags max tag kb distance (default 250).
---flip-scan, and --show-tags.
+--tag-r2 [val]     : Set --show-tags min tag r-squared (default 0.8)
-1 (default) = males coded 0/1, females 0/1/2 (A1 dosage)
+--tag-mode2        : Use two-column --show-tags (file mode) I/O format.
-2 = males coded 0/2
+--ld-xchr [code]   : Set Xchr model for --indep{-pairwise}, --r/--r2,
-3 = males coded 0/2, but females given double weighting
+--flip-scan, and --show-tags.
---blocks-max-kb [kbs]      : Set --blocks maximum haploblock span (def. 200).
+1 (default) = males coded 0/1, females 0/1/2 (A1 dosage)
---blocks-min-maf [cutoff]  : Adjust --blocks MAF minimum (default 0.05).
+2 = males coded 0/2
---blocks-strong-lowci [x]  : Set --blocks 'strong LD' CI thresholds (defaults
+3 = males coded 0/2, but females given double weighting
---blocks-strong-highci [x]   0.70 and 0.98).
+--blocks-max-kb [kbs]      : Set --blocks maximum haploblock span (def. 200).
---blocks-recomb-highci [x] : Set 'recombination' CI threshold (default 0.90).
+--blocks-min-maf [cutoff]  : Adjust --blocks MAF minimum (default 0.05).
---blocks-inform-frac [x]   : Force haploblock [strong LD pairs]:[total
+--blocks-strong-lowci [x]  : Set --blocks 'strong LD' CI thresholds (defaults
-informative pairs] ratios to be larger than this
+--blocks-strong-highci [x]   0.70 and 0.98).
-value (default 0.95).
+--blocks-recomb-highci [x] : Set 'recombination' CI threshold (default 0.90).
---distance-wts exp=[x]        : When computing genomic distances, assign each
+--blocks-inform-frac [x]   : Force haploblock [strong LD pairs]:[total
-variant a weight of (2q(1-q))^{-x}, where q
+informative pairs] ratios to be larger than this
-is the loaded or inferred MAF.
+value (default 0.95).
---read-dists [dist file] {id file} : Load a triangular binary distance matrix
+--distance-wts exp=[x]        : When computing genomic distances, assign each
-instead of recalculating from scratch.
+variant a weight of (2q(1-q))^{-x}, where q
---ppc-gap [val]    : Minimum number of base pairs, in thousands, between
+is the loaded or inferred MAF.
-informative pairs of markers used in --genome PPC test.
+--read-dists [dist file] {id file} : Load a triangular binary distance matrix
-500 if unspecified.
+instead of recalculating from scratch.
---min [cutoff]     : Specify minimum PI_HAT for inclusion in --genome report.
+--ppc-gap [val]    : Minimum number of base pairs, in thousands, between
---max [cutoff]     : Specify maximum PI_HAT for inclusion in --genome report.
+informative pairs of markers used in --genome PPC test.
---homozyg-match [] : Set minimum concordance across jointly homozygous
+500 if unspecified.
-variants for a pairwise allelic match to be declared.
+--min [cutoff]     : Specify minimum PI_HAT for inclusion in --genome report.
---pool-size [ct]   : Set minimum size of pools in '--homozyg group' report.
+--max [cutoff]     : Specify maximum PI_HAT for inclusion in --genome report.
---read-genome [fn] : Load --genome report for --cluster/--neighbour, instead
+--homozyg-match [] : Set minimum concordance across jointly homozygous
-of recalculating IBS and PPC test p-values from scratch.
+variants for a pairwise allelic match to be declared.
---ppc [p-val]    : Specify minimum PPC test p-value within a cluster.
+--pool-size [ct]   : Set minimum size of pools in '--homozyg group' report.
---mc [max size]  : Specify maximum cluster size.
+--read-genome [fn] : Load --genome report for --cluster/--neighbour, instead
---mcc [c1] [c2]  : Specify maximum case and control counts per cluster.
+of recalculating IBS and PPC test p-values from scratch.
---K [min count]  : Specify minimum cluster count.
+--ppc [p-val]    : Specify minimum PPC test p-value within a cluster.
---ibm [val]      : Specify minimum identity-by-missingness.
+--mc [max size]  : Specify maximum cluster size.
---match [f] {mv} : Use covariate values to restrict clustering.  Without
+--mcc [c1] [c2]  : Specify maximum case and control counts per cluster.
---match-type, two samples can only be in the same cluster
+--K [min count]  : Specify minimum cluster count.
-if all covariates match.  The optional second parameter
+--ibm [val]      : Specify minimum identity-by-missingness.
-specifies a covariate value to treat as missing.
+--match [f] {mv} : Use covariate values to restrict clustering.  Without
---match-type [f] : Refine interpretation of --match file.  The --match-type
+--match-type, two samples can only be in the same cluster
-file is expected to be a single line with as many entries
+if all covariates match.  The optional second parameter
-as the --match file has covariates; '0' entries specify
+specifies a covariate value to treat as missing.
-'negative matches' (i.e. samples with equal covariate
+--match-type [f] : Refine interpretation of --match file.  The --match-type
-values cannot be in the same cluster), '1' entries specify
+file is expected to be a single line with as many entries
-'positive matches' (default), and '-1' causes the
+as the --match file has covariates; '0' entries specify
-corresponding covariate to be ignored.
+'negative matches' (i.e. samples with equal covariate
---qmatch [f] {m} : Force all members of a cluster to have similar
+values cannot be in the same cluster), '1' entries specify
---qt [fname]       quantitative covariate values.  The --qmatch file contains
+'positive matches' (default), and '-1' causes the
-the covariate values, while the --qt file is a list of
+corresponding covariate to be ignored.
-nonnegative tolerances (and '-1's marking covariates to
+--qmatch [f] {m} : Force all members of a cluster to have similar
-skip).
+--qt [fname]       quantitative covariate values.  The --qmatch file contains
---pca-cluster-names [...] : These can be used individually or in combination
+the covariate values, while the --qt file is a list of
---pca-clusters [fname]      to define a list of clusters to use in the basic
+nonnegative tolerances (and '-1's marking covariates to
---pca computation.  (--pca-cluster-names expects
+skip).
-a space-delimited sequence of cluster names,
+--pca-cluster-names [...] : These can be used individually or in combination
-while --pca-clusters expects a file with one
+--pca-clusters [fname]      to define a list of clusters to use in the basic
-cluster name per line.)  All samples outside
+--pca computation.  (--pca-cluster-names expects
-those clusters will then be projected on to the
+a space-delimited sequence of cluster names,
-calculated PCs.
+while --pca-clusters expects a file with one
---mds-plot [dims] <by-cluster> <eigendecomp> <eigvals> :
+cluster name per line.)  All samples outside
-Multidimensional scaling analysis.  Requires --cluster.
+those clusters will then be projected on to the
---cell [thresh]  : Skip some --model tests when a contingency table entry is
+calculated PCs.
-smaller than the given threshold.
+--mds-plot [dims] <by-cluster> <eigendecomp> <eigvals> :
---condition [var ID] <dominant | recessive> : Add one variant as a --linear
+Multidimensional scaling analysis.  Requires --cluster.
-or --logistic covariate.
+--cell [thresh]  : Skip some --model tests when a contingency table entry is
---condition-list [f] <dominant | recessive> : Add variants named in the file
+smaller than the given threshold.
-as --linear/--logistic covs.
+--condition [var ID] <dominant | recessive> : Add one variant as a --linear
---parameters [...]  : Include only the given covariates/interactions in the
+or --logistic covariate.
---linear/--logistic models, identified by a list of
+--condition-list [f] <dominant | recessive> : Add variants named in the file
-1-based indices and/or ranges of them.
+as --linear/--logistic covs.
---tests <all> {...} : Perform a (joint) test on the specified term(s) in the
+--parameters [...]  : Include only the given covariates/interactions in the
---linear/--logistic model, identified by 1-based
+--linear/--logistic models, identified by a list of
-indices and/or ranges of them.  If permutation was
+1-based indices and/or ranges of them.
-requested, it is based on this test.
+--tests <all> {...} : Perform a (joint) test on the specified term(s) in the
-* Note that, when --parameters is also present, the
+--linear/--logistic model, identified by 1-based
-indices refer to the terms remaining AFTER pruning by
+indices and/or ranges of them.  If permutation was
---parameters.
+requested, it is based on this test.
-* You can use '--tests all' to include all terms.
+* Note that, when --parameters is also present, the
---vif [max VIF]     : Set VIF threshold for --linear multicollinearity check
+indices refer to the terms remaining AFTER pruning by
-(default 50).
+--parameters.
---xchr-model [code] : Set the X chromosome --linear/--logistic model.
+* You can use '--tests all' to include all terms.
-0 = skip sex and haploid chromosomes
+--vif [max VIF]     : Set VIF threshold for --linear multicollinearity check
-1 (default) = add sex as a covariate on X chromosome
+(default 50).
-2 = code male genotypes 0/2 instead of 0/1
+--xchr-model [code] : Set the X chromosome --linear/--logistic model.
-3 = test for interaction between genotype and sex
+0 = skip sex and haploid chromosomes
---lasso-select-covars {cov(s)...} : Subject some or all covariates to LASSO
+1 (default) = add sex as a covariate on X chromosome
-model selection.
+2 = code male genotypes 0/2 instead of 0/1
---adjust <gc> <log10> <qq-plot>   : Report some multiple-testing corrections.
+3 = test for interaction between genotype and sex
---lambda [val]   : Set genomic control lambda for --adjust.
+--lasso-select-covars {cov(s)...} : Subject some or all covariates to LASSO
---ci [size]      : Report confidence intervals for odds ratios.
+model selection.
---pfilter [val]  : Filter out association test results with higher p-values.
+--adjust <gc> <log10> <qq-plot>   : Report some multiple-testing corrections.
---aperm [min perms - 1] {max perms} {alpha} {beta} {init interval} {slope} :
+--lambda [val]   : Set genomic control lambda for --adjust.
-Set up to six parameters controlling adaptive permutation tests.
+--ci [size]      : Report confidence intervals for odds ratios.
-* The first two control the minimum and maximum number of permutations that
+--pfilter [val]  : Filter out association test results with higher p-values.
-may be run for each variant; default values are 5 and 1000000.
+--aperm [min perms - 1] {max perms} {alpha} {beta} {init interval} {slope} :
-* The next two control the early termination condition.  A
+Set up to six parameters controlling adaptive permutation tests.
-100% * (1 - beta/2T) confidence interval is calculated for each empirical
+* The first two control the minimum and maximum number of permutations that
-p-value, where T is the total number of variants; whenever this
+may be run for each variant; default values are 5 and 1000000.
-confidence interval doesn't contain alpha, the variant is exempted from
+* The next two control the early termination condition.  A
-further permutation testing.  Default values are 0 and 1e-4.
+100% * (1 - beta/2T) confidence interval is calculated for each empirical
-* The last two control when the early termination condition is checked.  If
+p-value, where T is the total number of variants; whenever this
-a check occurs at permutation #p, the next check occurs after
+confidence interval doesn't contain alpha, the variant is exempted from
-[slope]p + [init interval] more permutations (rounded down).  Default
+further permutation testing.  Default values are 0 and 1e-4.
-initial interval is 1, and default slope is 0.001.
+* The last two control when the early termination condition is checked.  If
---mperm-save     : Save best max(T) permutation test statistics.
+a check occurs at permutation #p, the next check occurs after
---mperm-save-all : Save all max(T) permutation test statistics.
+[slope]p + [init interval] more permutations (rounded down).  Default
---set-p [p-val]       : Adjust set test significant variant p-value ceiling
+initial interval is 1, and default slope is 0.001.
-(default 0.05).
+--mperm-save     : Save best max(T) permutation test statistics.
---set-r2 {v} <write>  : Adjust set test significant variant pairwise r^2
+--mperm-save-all : Save all max(T) permutation test statistics.
-ceiling (default 0.5).  'write' causes violating
+--set-p [p-val]       : Adjust set test significant variant p-value ceiling
-pairs to be dumped to {output prefix}.ldset.
+(default 0.05).
---set-max [ct]        : Adjust set test maximum # of significant variants
+--set-r2 {v} <write>  : Adjust set test significant variant pairwise r^2
-considered per set (default 5).
+ceiling (default 0.5).  'write' causes violating
---set-test-lambda [v] : Specify genomic control correction for set test.
+pairs to be dumped to {output prefix}.ldset.
---border [kbs]            : Extend --annotate range intervals by given # kbs.
+--set-max [ct]        : Adjust set test maximum # of significant variants
---annotate-snp-field [nm] : Set --annotate variant ID field name.
+considered per set (default 5).
---clump-p1 [pval] : Set --clump index var. p-value ceiling (default 1e-4).
+--set-test-lambda [v] : Specify genomic control correction for set test.
---clump-p2 [pval] : Set --clump secondary p-value threshold (default 0.01).
+--border [kbs]            : Extend --annotate range intervals by given # kbs.
---clump-r2 [r^2]  : Set --clump r^2 threshold (default 0.5).
+--annotate-snp-field [nm] : Set --annotate variant ID field name.
---clump-kb [kbs]  : Set --clump kb radius (default 250).
+--clump-p1 [pval] : Set --clump index var. p-value ceiling (default 1e-4).
---clump-snp-field [n...]  : Set --clump variant ID field name (default
+--clump-p2 [pval] : Set --clump secondary p-value threshold (default 0.01).
-'SNP').  With multiple field names, earlier names
+--clump-r2 [r^2]  : Set --clump r^2 threshold (default 0.5).
-take precedence over later ones.
+--clump-kb [kbs]  : Set --clump kb radius (default 250).
---clump-field [name...]   : Set --clump p-value field name (default 'P').
+--clump-snp-field [n...]  : Set --clump variant ID field name (default
---clump-allow-overlap     : Let --clump non-index vars. join multiple clumps.
+'SNP').  With multiple field names, earlier names
---clump-verbose           : Request extended --clump report.
+take precedence over later ones.
---clump-annotate [hdr...] : Include named extra fields in --clump-verbose and
+--clump-field [name...]   : Set --clump p-value field name (default 'P').
---clump-best reports.  (Field names can be
+--clump-allow-overlap     : Let --clump non-index vars. join multiple clumps.
-separated with spaces or commas.)
+--clump-verbose           : Request extended --clump report.
---clump-range [filename]  : Report overlaps between clumps and regions.
+--clump-annotate [hdr...] : Include named extra fields in --clump-verbose and
---clump-range-border [kb] : Stretch regions in --clump-range file.
+--clump-best reports.  (Field names can be
---clump-index-first       : Extract --clump index vars. from only first file.
+separated with spaces or commas.)
---clump-replicate         : Exclude clumps which contain secondary results
+--clump-range [filename]  : Report overlaps between clumps and regions.
-from only one file.
+--clump-range-border [kb] : Stretch regions in --clump-range file.
---clump-best              : Report best proxy for each --clump index var.
+--clump-index-first       : Extract --clump index vars. from only first file.
---meta-analysis-snp-field [n...] : Set --meta-analysis variant ID, A1/A2
+--clump-replicate         : Exclude clumps which contain secondary results
---meta-analysis-a1-field [n...]    allele, p-value, and/or effective sample
+from only one file.
---meta-analysis-a2-field [n...]    size field names.  Defauls are 'SNP',
+--clump-best              : Report best proxy for each --clump index var.
---meta-analysis-p-field [n...]     'A1', 'A2', 'P', and 'NMISS',
+--meta-analysis-snp-field [n...] : Set --meta-analysis variant ID, A1/A2
---meta-analysis-ess-field [n...]   respectively.  When multiple parameters
+--meta-analysis-a1-field [n...]    allele, p-value, and/or effective sample
-are given to these flags, earlier names
+--meta-analysis-a2-field [n...]    size field names.  Defauls are 'SNP',
-take precedence over later ones.
+--meta-analysis-p-field [n...]     'A1', 'A2', 'P', and 'NMISS',
-Note that, if the numbers of cases and
+--meta-analysis-ess-field [n...]   respectively.  When multiple parameters
-controls are unequal, effective sample
+are given to these flags, earlier names
-size should be
+take precedence over later ones.
-4 / (1/[# cases] + 1/[# controls]).
+Note that, if the numbers of cases and
---meta-analysis-report-dups      : When a variant appears multiple times in
+controls are unequal, effective sample
-in the same file, report that.
+size should be
---gene-list-border [kbs]   : Extend --gene-report regions by given # of kbs.
+4 / (1/[# cases] + 1/[# controls]).
---gene-subset [filename]   : Specify gene name subset for --gene-report.
+--meta-analysis-report-dups      : When a variant appears multiple times in
---gene-report-snp-field [] : Set --gene-report variant ID field name (default
+in the same file, report that.
-'SNP').  Only relevant with --extract.
+--gene-list-border [kbs]   : Extend --gene-report regions by given # of kbs.
---gap [kbs]      : Set '--fast-epistasis case-only' min. gap (default 1000).
+--gene-subset [filename]   : Specify gene name subset for --gene-report.
---epi1 [p-value] : Set --{fast-}epistasis reporting threshold (default
+--gene-report-snp-field [] : Set --gene-report variant ID field name (default
-5e-6 for 'boost', 1e-4 otherwise).
+'SNP').  Only relevant with --extract.
---epi2 [p-value] : Set threshold for contributing to SIG_E count (def. 0.01).
+--gap [kbs]      : Set '--fast-epistasis case-only' min. gap (default 1000).
---je-cellmin [n] : Set required number of observations per 3x3x2 contingency
+--epi1 [p-value] : Set --{fast-}epistasis reporting threshold (default
-table cell for joint-effects test (default 5).
+5e-6 for 'boost', 1e-4 otherwise).
---q-score-range [range file] [data file] {i} {j} <header> :
+--epi2 [p-value] : Set threshold for contributing to SIG_E count (def. 0.01).
-Apply --score to subset(s) of variants in the primary score list based
+--je-cellmin [n] : Set required number of observations per 3x3x2 contingency
-on e.g. p-value ranges.
+table cell for joint-effects test (default 5).
-* The first file should have range labels in the first column, p-value
+--q-score-range [range file] [data file] {i} {j} <header> :
-lower bounds in the second column, and upper bounds in the third column.
+Apply --score to subset(s) of variants in the primary score list based
-Lines with too few entries, or nonnumeric values in the second or third
+on e.g. p-value ranges.
-column, are ignored.
+* The first file should have range labels in the first column, p-value
-* The second file should contain a variant ID and a p-value on each
+lower bounds in the second column, and upper bounds in the third column.
-nonempty line (except possibly the first).  Variant IDs are read from
+Lines with too few entries, or nonnumeric values in the second or third
-column #i and p-values are read from column #j, where i defaults to 1 and
+column, are ignored.
-j defaults to i+1.  The 'header' modifier causes the first nonempty line
+* The second file should contain a variant ID and a p-value on each
-of this file to be skipped.
+nonempty line (except possibly the first).  Variant IDs are read from
---parallel [k] [n] : Divide the output matrix into n pieces, and only compute
+column #i and p-values are read from column #j, where i defaults to 1 and
-the kth piece.  The primary output file will have the
+j defaults to i+1.  The 'header' modifier causes the first nonempty line
-piece number included in its name, e.g. plink.rel.13 or
+of this file to be skipped.
-plink.rel.13.gz if k is 13.  Concatenating these files
+--parallel [k] [n] : Divide the output matrix into n pieces, and only compute
-in order will yield the full matrix of interest.  (Yes,
+the kth piece.  The primary output file will have the
-this can be done before unzipping.)
+piece number included in its name, e.g. plink.rel.13 or
-N.B. This generally cannot be used to directly write a
+plink.rel.13.gz if k is 13.  Concatenating these files
-symmetric square matrix.  Choose square0 or triangle
+in order will yield the full matrix of interest.  (Yes,
-shape instead, and postprocess as necessary.
+this can be done before unzipping.)
---memory [val]     : Set size, in MB, of initial workspace malloc attempt.
+N.B. This generally cannot be used to directly write a
-(Practically mandatory when using GNU parallel.)
+symmetric square matrix.  Choose square0 or triangle
---threads [val]    : Set maximum number of concurrent threads.
+shape instead, and postprocess as necessary.
-This has one known limitation: some BLAS/LAPACK linear
+--memory [val]     : Set size, in MB, of initial workspace malloc attempt.
-algebra operations are multithreaded in a way that PLINK
+(Practically mandatory when using GNU parallel.)
-cannot control.  If this is problematic, you should
+--threads [val]    : Set maximum number of concurrent threads.
-recompile against single-threaded BLAS/LAPACK.
+This has one known limitation: some BLAS/LAPACK linear
---d [char]         : Change variant/covariate range delimiter (normally '-').
+algebra operations are multithreaded in a way that PLINK
---seed [val...]    : Set random number seed(s).  Each value must be an
+cannot control.  If this is problematic, you should
-integer between 0 and 4294967295 inclusive.
+recompile against single-threaded BLAS/LAPACK.
---perm-batch-size [val] : Set number of permutations per batch for some
+--d [char]         : Change variant/covariate range delimiter (normally '-').
-permutation tests.
+--seed [val...]    : Set random number seed(s).  Each value must be an
---output-min-p [p] : Specify minimum p-value to write to reports.
+integer between 0 and 4294967295 inclusive.
---debug            : Use slower, more crash-resistant logging method.
+--perm-batch-size [val] : Set number of permutations per batch for some
+permutation tests.
-Primary methods paper:
+--output-min-p [p] : Specify minimum p-value to write to reports.
-Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015)
+--debug            : Use slower, more crash-resistant logging method.
-Second-generation PLINK: rising to the challenge of larger and richer datasets.
-GigaScience, 4.
+Primary methods paper:
+Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015)
-For further documentation and support, consult the main webpage
+Second-generation PLINK: rising to the challenge of larger and richer datasets.
-(https://www.cog-genomics.org/plink2 ) and/or the mailing list
+GigaScience, 4.
-(https://groups.google.com/d/forum/plink2-users ).
+For further documentation and support, consult the main webpage
+(https://www.cog-genomics.org/plink2 ) and/or the mailing list
+(https://groups.google.com/d/forum/plink2-users ).
 ]]></help>
 <citations>
 <citation type="doi">10.1186/s13742-015-0047-8</citation>
 <citation type="bibtex">@ARTICLE{Blankenberg19-plink,

Mercurial > repos > blankenberg > plink

comparison plink.xml @ 3:4c3690a9d729 draft default tip