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| author | devteam |
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| date | Thu, 27 Sep 2012 13:37:59 -0400 |
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<tool id="cg_mkvcf" name="mkvcf(beta) 1.6" version="1.0.0"> <!-- This tool creates a GUI for the mkvcf function of cgatools from Complete Genomics, Inc. written 7-31-2012 by bcrain@completegenomics.com --> <description>converts to vcf</description> <command interpreter="perl"> <!--run wrapper script--> mkvcf_wrapper.pl --reference $crr.fields.path --output $output --genomes $count.genomes --source $count.sources.source --datasource $count.sources.data_sources.data_source #if $count.sources.data_sources.data_source=="in" #for $m in $count.sources.data_sources.files --input $m.input #end for #else --input $count.sources.data_sources.input #end if #if $count.sources.source=="masterVar" or $count.sources.source=="masterVar,CNV" $count.sources.nocalls --calibration $count.sources.calibration #else if $count.sources.source=="SV" --jctscore $count.sources.jctscore --jctside $count.sources.jctside --jctdistance $count.sources.jctdistance --jctlength $count.sources.jctlength $count.sources.jctpriority $count.sources.jcttumor #else if $count.sources.source=="masterVar,CNV,SV" or $count.sources.source=="masterVar,CNV,SV,MEI" $count.sources.nocalls --calibration $count.sources.calibration --jctscore $count.sources.jctscore --jctside $count.sources.jctside --jctdistance $count.sources.jctdistance --jctlength $count.sources.jctlength $count.sources.jctpriority $count.sources.jcttumor #end if --fields $count.sources.fields </command> <outputs> <data format="vcf" name="output" label="${tool.name} output"/> </outputs> <inputs> <!--form field to select crr file--> <param name="crr" type="select" label="Reference genome (.crr file)"> <options from_data_table="cg_crr_files" /> </param> <!--select number of genomes - determines which input sources to show--> <conditional name="count"> <param name="genomes" type="select" label="Select the number of genomes to add to the vcf file" help="Note: multi-genome vcfs (2 or more genomes) can only be generated for format version 2.0 and up"> <option value="1" selected="true">1 - allowed data sources are masterVar, CNV, SV, MEI</option> <option value="2">2 - allowed data sources are masterVar, CNV, SV (format v2.x)</option> <option value="3">3 or more - allowed data sources are masterVar, CNV (format v2.x)</option> </param> <when value="1"> <!--form field to select input sources--> <conditional name="sources"> <param name="source" type="select" label="Data sources to be included for this genome"> <option value="masterVar,CNV,SV,MEI" selected="true">masterVar + CNV + SV + MEI</option> <option value="masterVar">masterVar</option> <option value="CNV">CNV</option> <option value="SV">SV</option> <option value="MEI">MEI</option> </param> <when value="masterVar,CNV,SV,MEI"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="out" selected="true">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="Genome root directory" size="200" help="Enter full path /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01)."> <validator type="empty_field" message="You must supply the genome root directory"/> </param> </when> </conditional> <!--form field to select no-calls--> <param name="nocalls" type="select" label="Include no-calls?"> <option value="" selected="true">no</option> <option value="--nocalls">yes</option> </param> <!--form field to enter calibration directory--> <param name="calibration" type="text" size="300" label="Directory calibration data (/path/calibration-root)" help="The directory containing calibration data. For example, there should exist a file calibration-root/0.0.0/metrics.tsv. Calibration data can be downloaded from ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz"/> <!--form fields junction threshold options--> <param name="jctscore" type="integer" value="10" label="Junction score thresholds (discordant mate pair count) (default 10)"> <validator type="empty_field" message="You must enter a value, for the default value enter 10" /> </param> <param name="jctside" type="integer" value="70" label="Junction side length threshold (default 70)"> <validator type="empty_field" message="You must enter a value, for the default value enter 70" /> </param> <param name="jctdistance" type="integer" value="200" label="Distance tolerance for junction compatibility (default 200)"> <validator type="empty_field" message="You must enter a value, for the default value enter 200" /> </param> <param name="jctlength" type="integer" value="500" label="Length threshold for compatible junctions (default 500)"> <validator type="empty_field" message="You must enter a value, for the default value enter 500" /> </param> <!--form field to select junction confidence in tumors--> <param name="jctpriority" type="select" label="Use normal junction priority for vcf output?"> <option value="" selected="true">no</option> <option value="--jctpriority">yes</option> </param> <!--form field to select junction confidence in tumors--> <param name="jcttumor" type="select" label="Use high confidence junctions for tumors?"> <option value="" selected="true">no</option> <option value="--jcttumor">yes</option> </param> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="NS">NS - Number of samples</option> <option value="AN">AN - Total number of alleles in called genotypes</option> <option value="AC">AC - Allele count in genotypes</option> <option value="CGA_XR">CGA_XR - External database reference</option> <option value="CGA_FI">CGA_FI - Functional impact</option> <option value="CGA_PFAM">CGA_PFAM - PFAM domain </option> <option value="CGA_MIRB">CGA_MIRB - miRBaseId</option> <option value="CGA_SDO">CGA_SDO - Depth of overlapping segmental duplications</option> <option value="CGA_RPT">CGA_RPT - Overlapping repeatMasker annotations</option> <option value="GT">GT - Genotype</option> <option value="PS">PS - Phase set</option> <option value="FT">FT - Sample genotype filters</option> <option value="GL">GL - Genotype likelihoods</option> <option value="CGA_CEHQ">CGA_CEHQ - Calibrated haplotype quality based on EAF assumption</option> <option value="CGA_CEGL">CGA_CEGL - Genotype likelihoods based on CEHQ</option> <option value="SS">SS - Somatic status</option> <option value="HQ">HQ - Haplotype quality</option> <option value="EHQ">EHQ - Haplotype quality based on EAF assumption</option> <option value="GQ">GQ - Genotype quality</option> <option value="DP">DP - Total read depth</option> <option value="AD">AD - Allelic depths</option> <option value="CGA_RDP">CGA_RDP - Read depth in reference</option> <option value="CGA_ODP">CGA_ODP - Other total read depth: somatic comparison</option> <option value="CGA_OAD">CGA_OAD - Other allelic depths: somatic comparison</option> <option value="CGA_ORDP">CGA_ORDP - Other reference depth: somatic comparison </option> <option value="CGA_SOMC">CGA_SOMC - Somatic Category</option> <option value="CGA_SOMR">CGA_SOMR - Somatic Rank</option> <option value="CGA_SOMS">CGA_SOMS - Somatic Score</option> <option value="CGA_GP">CGA_GP - Normalized mean GC corrected coverage</option> <option value="CGA_NP">CGA_NP - Normalized mean coverage for 2k window</option> <option value="CGA_CP">CGA_CP - Diploid-model ploidy call for segment including this interval</option> <option value="CGA_PS">CGA_PS - Diploid-model called ploidy score</option> <option value="CGA_CT">CGA_CT - Diploid-model CNV type</option> <option value="CGA_TS">CGA_TS - Diploid-model CNV type score</option> <option value="CGA_CL">CGA_CL - Nondiploid-model called level</option> <option value="CGA_LS">CGA_LS - Nondiploid-model called level score</option> <option value="CGA_SCL">CGA_SCL - Nondiploid-model somatic called level</option> <option value="CGA_SLS">CGA_SLS - Non-diploid-model somatic called level score</option> <option value="CGA_LAF">CGA_LAF - Lesser Allele Fraction estimate, 100k window</option> <option value="CGA_LLAF">CGA_LLAF - Lesser Allele Fraction lower bound, 100k window</option> <option value="CGA_ULAF">CGA_ULAF - Lesser Allele Fraction upper bound, 100k window</option> <option value="SVTYPE">SVTYPE - Type of structural variation</option> <option value="CGA_BF">CGA_BF - Frequency in set of baseline genomes</option> <option value="CGA_MEDEL">CGA_MEDEL - Mobile element deletion</option> <option value="MATEID">MATEID - ID of mate breakend</option> <option value="CGA_BNDG">CGA_BNDG - Transcript name and strand of genes containing breakend</option> <option value="CGA_BNDGO">CGA_BNDGO - Transcript name and strand of genes containing mate breakend</option> <option value="CGA_BNDP">CGA_BNDP - Precision of breakend</option> <option value="CGA_BNDMPC">CGA_BNDMPC - Mate pair count supporting a breakend</option> <option value="CGA_BNDPOS">CGA_BNDPOS - Position of breakend as detected in individual genome</option> <option value="CGA_BNDDEF">CGA_BNDDEF - Breakend definition in individual genome</option> <option value="CGA_IS">CGA_IS - Measure of confidence that there is a mobile element insertion</option> <option value="CGA_IDC">CGA_IDC - Count of paired ends consistently indicating a mobile element insertion</option> <option value="CGA_IDCL">CGA_IDCL - Count of paired ends indicating a mobile element insertion anchored 5'</option> <option value="CGA_IDCR">CGA_IDCR - Count of paired ends indicating a mobile element insertion anchored 3'</option> <option value="CGA_RDC">CGA_RDC - Count of paired ends supporting the presence of a reference allele</option> <option value="CGA_NBET">CGA_NBET - Next-best estimate of type of MEI</option> <option value="CGA_ETS">CGA_ETS - Measure of confidence that the ElementType (MEINFO:NAME) is correct</option> <option value="CGA_KES">CGA_KES - Fraction of known MEI with at least as good an InsertionScore</option> </param> </when> <when value="masterVar"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where is the input file?"> <option value="in" selected="true">imported into Galaxy</option> <option value="out">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="in"> <!--form field to select mastervar files--> <repeat name="files" title="MasterVar file" min="1" max="1"> <param name="input" type="data" format="cg_mastervar" label="Dataset"> <validator type="dataset_ok_validator" /> <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" metadata_name="dbkey" metadata_column="1" message="cgatools is not currently available for this build."/> </param> </repeat> </when> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="Genome root directory or masterVar file" size="200" help="Enter full path /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01), or /path/masterVarfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01/ASM/masterVarBeta-GS00000YYYY-ASM.tsv.bz2)."> <validator type="empty_field" message="You must supply the genome root directory or masterVar file"/> </param> </when> </conditional> <!--form field to select no-calls--> <param name="nocalls" type="select" label="Include no-calls?"> <option value="" selected="true">no</option> <option value="--nocalls">yes</option> </param> <!--form field to enter calibration directory--> <param name="calibration" type="text" size="300" label="Directory calibration data (/path/calibration-root)" help="The directory containing calibration data. For example, there should exist a file calibration-root/0.0.0/metrics.tsv. Calibration data can be downloaded from ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz"/> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="NS">NS - Number of samples</option> <option value="AN">AN - Total number of alleles in called genotypes</option> <option value="AC">AC - Allele count in genotypes</option> <option value="CGA_XR">CGA_XR - External database reference</option> <option value="CGA_FI">CGA_FI - Functional impact</option> <option value="CGA_PFAM">CGA_PFAM - PFAM domain </option> <option value="CGA_MIRB">CGA_MIRB - miRBaseId</option> <option value="CGA_SDO">CGA_SDO - Depth of overlapping segmental duplications</option> <option value="CGA_RPT">CGA_RPT - Overlapping repeatMasker annotations</option> <option value="GT">GT - Genotype</option> <option value="PS">PS - Phase set</option> <option value="FT">FT - Sample genotype filters</option> <option value="GL">GL - Genotype likelihoods</option> <option value="CGA_CEHQ">CGA_CEHQ - Calibrated haplotype quality based on EAF assumption</option> <option value="CGA_CEGL">CGA_CEGL - Genotype likelihoods based on CEHQ</option> <option value="SS">SS - Somatic status</option> <option value="HQ">HQ - Haplotype quality</option> <option value="EHQ">EHQ - Haplotype quality based on EAF assumption</option> <option value="GQ">GQ - Genotype quality</option> <option value="DP">DP - Total read depth</option> <option value="AD">AD - Allelic depths</option> <option value="CGA_RDP">CGA_RDP - Read depth in reference</option> <option value="CGA_ODP">CGA_ODP - Other total read depth: somatic comparison</option> <option value="CGA_OAD">CGA_OAD - Other allelic depths: somatic comparison</option> <option value="CGA_ORDP">CGA_ORDP - Other reference depth: somatic comparison </option> <option value="CGA_SOMC">CGA_SOMC - Somatic Category</option> <option value="CGA_SOMR">CGA_SOMR - Somatic Rank</option> <option value="CGA_SOMS">CGA_SOMS - Somatic Score</option> </param> </when> <when value="CNV"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="out" selected="true">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="Genome root directory" size="200" help="Enter full path /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01)."> <validator type="empty_field" message="You must supply the genome root directory"/> </param> </when> </conditional> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="GT">GT - Genotype</option> <option value="CGA_GP">CGA_GP - Normalized mean GC corrected coverage</option> <option value="CGA_NP">CGA_NP - Normalized mean coverage for 2k window</option> <option value="CGA_CP">CGA_CP - Diploid-model ploidy call for segment</option> <option value="CGA_PS">CGA_PS - Diploid-model called ploidy score</option> <option value="CGA_CT">CGA_CT - Diploid-model CNV type</option> <option value="CGA_TS">CGA_TS - Diploid-model CNV type score</option> <option value="CGA_CL">CGA_CL - Nondiploid-model called level</option> <option value="CGA_LS">CGA_LS - Nondiploid-model called level score</option> <option value="CGA_SCL">CGA_SCL - Nondiploid-model somatic called level</option> <option value="CGA_SLS">CGA_SLS - Non-diploid-model somatic called level score</option> <option value="CGA_LAF">CGA_LAF - Lesser Allele Fraction estimate, 100k window</option> <option value="CGA_LLAF">CGA_LLAF - Lesser Allele Fraction lower bound, 100k window</option> <option value="CGA_ULAF">CGA_ULAF - Lesser Allele Fraction upper bound, 100k window</option> </param> </when> <when value="SV"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="in" selected="true">imported into Galaxy</option> <option value="out">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="in"> <!--form field to select SV file--> <repeat name="files" title="SV file" min="1" max="1"> <param name="input" type="data" format="tabular" label="Dataset"> <validator type="dataset_ok_validator" /> <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" metadata_name="dbkey" metadata_column="1" message="cgatools is not currently available for this build."/> </param> </repeat> </when> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="Genome root directory or SV file" size="200" help="Enter full path /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01), or /path/SVfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01/ASM/SV/allJunctionsBeta-GS00000YYYY-ASM.tsv)."> <validator type="empty_field" message="You must supply the genome root directory or SV file"/> </param> </when> </conditional> <!--form fields junction threshold options--> <param name="jctscore" type="integer" value="10" label="Junction score thresholds (discordant mate pair count) (default 10)"> <validator type="empty_field" message="You must enter a value, for the default value enter 10" /> </param> <param name="jctside" type="integer" value="70" label="Junction side length threshold (default 70)"> <validator type="empty_field" message="You must enter a value, for the default value enter 70" /> </param> <param name="jctdistance" type="integer" value="200" label="Distance tolerance for junction compatibility (default 200)"> <validator type="empty_field" message="You must enter a value, for the default value enter 200" /> </param> <param name="jctlength" type="integer" value="500" label="Length threshold for compatible junctions (default 500)"> <validator type="empty_field" message="You must enter a value, for the default value enter 500" /> </param> <!--form field to select junction confidence in tumors--> <param name="jctpriority" type="select" label="Use normal junction priority for vcf output?"> <option value="" selected="true">no</option> <option value="--jctpriority">yes</option> </param> <!--form field to select junction confidence in tumors--> <param name="jcttumor" type="select" label="Use high confidence junctions for tumors?"> <option value="" selected="true">no</option> <option value="--jcttumor">yes</option> </param> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="GT">GT - Genotype</option> <option value="FT">FT - Sample genotype filters</option> <option value="NS">NS - Number of samples</option> <option value="CGA_XR">CGA_XR - External database reference</option> <option value="SVTYPE">SVTYPE - Type of structural variation</option> <option value="CGA_BF">CGA_BF - Frequency in set of baseline genomes</option> <option value="CGA_MEDEL">CGA_MEDEL - Mobile element deletion</option> <option value="MATEID">MATEID - ID of mate breakend</option> <option value="CGA_BNDG">CGA_BNDG - Transcript name and strand of genes containing breakend</option> <option value="CGA_BNDGO">CGA_BNDGO - Transcript name and strand of genes containing mate breakend</option> <option value="CGA_BNDP">CGA_BNDP - Precision of breakend</option> <option value="CGA_BNDMPC">CGA_BNDMPC - Mate pair count supporting a breakend</option> <option value="CGA_BNDPOS">CGA_BNDPOS - Position of breakend as detected in individual genome</option> <option value="CGA_BNDDEF">CGA_BNDDEF - Breakend definition in individual genome</option> </param> </when> <when value="MEI"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="out" selected="true">located outside Galaxy</option> </param> <when value="out"> <!--form field to select outside list of genome directories or mastervar files--> <param name="input" type="text" label="Genome root directory" size="200" help="Enter full path /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01)."> <validator type="empty_field" message="You must supply the genome root directory"/> </param> </when> </conditional> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="GT">GT - Genotype</option> <option value="FT">FT - Sample genotype filters</option> <option value="CGA_IS">CGA_IS - Measure of confidence that there is a mobile element insertion</option> <option value="CGA_IDC">CGA_IDC - Count of paired ends consistently indicating a mobile element insertion</option> <option value="CGA_IDCL">CGA_IDCL - Count of paired ends indicating a mobile element insertion, anchored 5'</option> <option value="CGA_IDCR">CGA_IDCR - Count of paired ends indicating a mobile element insertion, anchored 3'</option> <option value="CGA_RDC">CGA_RDC - Count of paired ends supporting the presence of a reference allele</option> <option value="CGA_NBET">CGA_NBET - Next-best estimate of type of MEI</option> <option value="CGA_ETS">CGA_ETS - Measure of confidence that the ElementType (MEINFO:NAME) is correct</option> <option value="CGA_KES">CGA_KES - Fraction of known MEI with at least as good an InsertionScore</option> </param> </when> </conditional> </when> <when value="2"> <!--form field to select input sources--> <conditional name="sources"> <param name="source" type="select" label="Data sources to be included for each genome"> <option value="masterVar,CNV,SV" selected="true">masterVar + CNV + SV</option> <option value="masterVar">masterVar</option> <option value="CNV">CNV</option> <option value="SV">SV</option> </param> <when value="masterVar,CNV,SV"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="out" selected="true">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="File with list of genome root directories" size="200" help="Enter file name with full path (/path/file). This file should contain a list of genome root directory names, one per line in the format /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01). For normal/tumor comparisons list the baseline genome first."> <validator type="empty_field" message="You must supply the list of genome root directories"/> </param> </when> </conditional> <!--form field to select no-calls--> <param name="nocalls" type="select" label="Include no-calls?"> <option value="" selected="true">no</option> <option value="--nocalls">yes</option> </param> <!--form field to enter calibration directory--> <param name="calibration" type="text" size="300" label="Directory calibration data (/path/calibration-root)" help="The directory containing calibration data. For example, there should exist a file calibration-root/0.0.0/metrics.tsv. Calibration data can be downloaded from ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz"/> <!--form fields junction threshold options--> <param name="jctscore" type="integer" value="10" label="Junction score thresholds (discordant mate pair count) (default 10)"> <validator type="empty_field" message="You must enter a value, for the default value enter 10" /> </param> <param name="jctside" type="integer" value="70" label="Junction side length threshold (default 70)"> <validator type="empty_field" message="You must enter a value, for the default value enter 70" /> </param> <param name="jctdistance" type="integer" value="200" label="Distance tolerance for junction compatibility (default 200)"> <validator type="empty_field" message="You must enter a value, for the default value enter 200" /> </param> <param name="jctlength" type="integer" value="500" label="Length threshold for compatible junctions (default 500)"> <validator type="empty_field" message="You must enter a value, for the default value enter 500" /> </param> <!--form field to select junction confidence in tumors--> <param name="jctpriority" type="select" label="Use normal junction priority for vcf output?"> <option value="" selected="true">no</option> <option value="--jctpriority">yes</option> </param> <!--form field to select junction confidence in tumors--> <param name="jcttumor" type="select" label="Use high confidence junctions for tumors?"> <option value="" selected="true">no</option> <option value="--jcttumor">yes</option> </param> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="NS">NS - Number of samples</option> <option value="AN">AN - Total number of alleles in called genotypes</option> <option value="AC">AC - Allele count in genotypes</option> <option value="CGA_XR">CGA_XR - External database reference</option> <option value="CGA_FI">CGA_FI - Functional impact</option> <option value="CGA_PFAM">CGA_PFAM - PFAM domain </option> <option value="CGA_MIRB">CGA_MIRB - miRBaseId</option> <option value="CGA_SDO">CGA_SDO - Depth of overlapping segmental duplications</option> <option value="CGA_RPT">CGA_RPT - Overlapping repeatMasker annotations</option> <option value="GT">GT - Genotype</option> <option value="PS">PS - Phase set</option> <option value="FT">FT - Sample genotype filters</option> <option value="GL">GL - Genotype likelihoods</option> <option value="CGA_CEHQ">CGA_CEHQ - Calibrated haplotype quality based on EAF assumption</option> <option value="CGA_CEGL">CGA_CEGL - Genotype likelihoods based on CEHQ</option> <option value="SS">SS - Somatic status</option> <option value="HQ">HQ - Haplotype quality</option> <option value="EHQ">EHQ - Haplotype quality based on EAF assumption</option> <option value="GQ">GQ - Genotype quality</option> <option value="DP">DP - Total read depth</option> <option value="AD">AD - Allelic depths</option> <option value="CGA_RDP">CGA_RDP - Read depth in reference</option> <option value="CGA_ODP">CGA_ODP - Other total read depth: somatic comparison</option> <option value="CGA_OAD">CGA_OAD - Other allelic depths: somatic comparison</option> <option value="CGA_ORDP">CGA_ORDP - Other reference depth: somatic comparison </option> <option value="CGA_SOMC">CGA_SOMC - Somatic Category</option> <option value="CGA_SOMR">CGA_SOMR - Somatic Rank</option> <option value="CGA_SOMS">CGA_SOMS - Somatic Score</option> <option value="CGA_GP">CGA_GP - Normalized mean GC corrected coverage</option> <option value="CGA_NP">CGA_NP - Normalized mean coverage for 2k window</option> <option value="CGA_CP">CGA_CP - Diploid-model ploidy call for segment</option> <option value="CGA_PS">CGA_PS - Diploid-model called ploidy score</option> <option value="CGA_CT">CGA_CT - Diploid-model CNV type</option> <option value="CGA_TS">CGA_TS - Diploid-model CNV type score</option> <option value="CGA_CL">CGA_CL - Nondiploid-model called level</option> <option value="CGA_LS">CGA_LS - Nondiploid-model called level score</option> <option value="CGA_SCL">CGA_SCL - Nondiploid-model somatic called level</option> <option value="CGA_SLS">CGA_SLS - Non-diploid-model somatic called level score</option> <option value="CGA_LAF">CGA_LAF - Lesser Allele Fraction estimate, 100k window</option> <option value="CGA_LLAF">CGA_LLAF - Lesser Allele Fraction lower bound, 100k window</option> <option value="CGA_ULAF">CGA_ULAF - Lesser Allele Fraction upper bound, 100k window</option> <option value="SVTYPE">SVTYPE - Type of structural variation</option> <option value="CGA_BF">CGA_BF - Frequency in set of baseline genomes</option> <option value="CGA_MEDEL">CGA_MEDEL - Mobile element deletion</option> <option value="MATEID">MATEID - ID of mate breakend</option> <option value="CGA_BNDG">CGA_BNDG - Transcript name and strand of genes containing breakend</option> <option value="CGA_BNDGO">CGA_BNDGO - Transcript name and strand of genes containing mate breakend</option> <option value="CGA_BNDP">CGA_BNDP - Precision of breakend</option> <option value="CGA_BNDMPC">CGA_BNDMPC - Mate pair count supporting a breakend</option> <option value="CGA_BNDPOS">CGA_BNDPOS - Position of breakend as detected in individual genome</option> <option value="CGA_BNDDEF">CGA_BNDDEF - Breakend definition in individual genome</option> </param> </when> <when value="masterVar"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="in" selected="true">imported into Galaxy</option> <option value="out">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="in"> <!--form field to select input files--> <repeat name="files" title="MasterVar file" min="1" max="2"> <param name="input" type="data" format="cg_mastervar" label="Dataset"> <validator type="dataset_ok_validator"/> <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" metadata_name="dbkey" metadata_column="1" message="cgatools is not currently available for this build."/> </param> </repeat> </when> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="File with list of genome root directories or masterVar files" size="200" help="Enter file name with full path (/path/file). This file should contain a list of genome root directory names, one per line in the format /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01), or a list of masterVar files, one per line in the format /path/masterVarfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01/ASM/masterVarBeta-GS00000YYYY-ASM.tsv.bz2)."> <validator type="empty_field" message="You must supply the list of genome root directories or masterVar files"/> </param> </when> </conditional> <!--form field to select no-calls--> <param name="nocalls" type="select" label="Include no-calls?"> <option value="" selected="true">no</option> <option value="--nocalls">yes</option> </param> <!--form field to enter calibration directory--> <param name="calibration" type="text" size="300" label="Directory calibration data (/path/calibration-root)" help="The directory containing calibration data. For example, there should exist a file calibration-root/0.0.0/metrics.tsv. Calibration data can be downloaded from ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz"/> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="NS">NS - Number of samples</option> <option value="AN">AN - Total number of alleles in called genotypes</option> <option value="AC">AC - Allele count in genotypes</option> <option value="CGA_XR">CGA_XR - External database reference</option> <option value="CGA_FI">CGA_FI - Functional impact</option> <option value="CGA_PFAM">CGA_PFAM - PFAM domain </option> <option value="CGA_MIRB">CGA_MIRB - miRBaseId</option> <option value="CGA_SDO">CGA_SDO - Depth of overlapping segmental duplications</option> <option value="CGA_RPT">CGA_RPT - Overlapping repeatMasker annotations</option> <option value="GT">GT - Genotype</option> <option value="PS">PS - Phase set</option> <option value="FT">FT - Sample genotype filters</option> <option value="GL">GL - Genotype likelihoods</option> <option value="CGA_CEHQ">CGA_CEHQ - Calibrated haplotype quality based on EAF assumption</option> <option value="CGA_CEGL">CGA_CEGL - Genotype likelihoods based on CEHQ</option> <option value="SS">SS - Somatic status</option> <option value="HQ">HQ - Haplotype quality</option> <option value="EHQ">EHQ - Haplotype quality based on EAF assumption</option> <option value="GQ">GQ - Genotype quality</option> <option value="DP">DP - Total read depth</option> <option value="AD">AD - Allelic depths</option> <option value="CGA_RDP">CGA_RDP - Read depth in reference</option> <option value="CGA_ODP">CGA_ODP - Other total read depth: somatic comparison</option> <option value="CGA_OAD">CGA_OAD - Other allelic depths: somatic comparison</option> <option value="CGA_ORDP">CGA_ORDP - Other reference depth: somatic comparison </option> <option value="CGA_SOMC">CGA_SOMC - Somatic Category</option> <option value="CGA_SOMR">CGA_SOMR - Somatic Rank</option> <option value="CGA_SOMS">CGA_SOMS - Somatic Score</option> </param> </when> <when value="CNV"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="out" selected="true">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="File with list of genome root directories" size="200" help="Enter file name with full path (/path/file). This file should contain a list of genome root directory names, one per line in the format /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01)."> <validator type="empty_field" message="You must supply the list of genome root directories"/> </param> </when> </conditional> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="GT">GT - Genotype</option> <option value="CGA_GP">CGA_GP - Normalized mean GC corrected coverage</option> <option value="CGA_NP">CGA_NP - Normalized mean coverage for 2k window</option> <option value="CGA_CP">CGA_CP - Diploid-model ploidy call for segment</option> <option value="CGA_PS">CGA_PS - Diploid-model called ploidy score</option> <option value="CGA_CT">CGA_CT - Diploid-model CNV type</option> <option value="CGA_TS">CGA_TS - Diploid-model CNV type score</option> <option value="CGA_CL">CGA_CL - Nondiploid-model called level</option> <option value="CGA_LS">CGA_LS - Nondiploid-model called level score</option> <option value="CGA_SCL">CGA_SCL - Nondiploid-model somatic called level</option> <option value="CGA_SLS">CGA_SLS - Non-diploid-model somatic called level score</option> <option value="CGA_LAF">CGA_LAF - Lesser Allele Fraction estimate, 100k window</option> <option value="CGA_LLAF">CGA_LLAF - Lesser Allele Fraction lower bound, 100k window</option> <option value="CGA_ULAF">CGA_ULAF - Lesser Allele Fraction upper bound, 100k window</option> </param> </when> <when value="SV"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="in" selected="true">imported into Galaxy</option> <option value="out">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="in"> <!--form field to select mastervar files--> <repeat name="files" title="SV files" min="1" max="2"> <param name="input" type="data" format="tabular" label="Dataset"> <validator type="dataset_ok_validator" /> <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" metadata_name="dbkey" metadata_column="1" message="cgatools is not currently available for this build."/> </param> </repeat> </when> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="File with list of genome root directories or SV files" size="200" help="Enter file name with full path (/path/file). This file should contain a list of genome root directory names, one per line in the format /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01), or a list of SV files, one per line in the format /path/SVfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01/ASM/SV/allJunctionsBeta-GS00000YYYY-ASM.tsv)."> <validator type="empty_field" message="You must supply the list of genome root directories or SV files"/> </param> </when> </conditional> <!--form fields junction threshold options--> <param name="jctscore" type="integer" value="10" label="Junction score thresholds (discordant mate pair count) (default 10)"> <validator type="empty_field" message="You must enter a value, for the default value enter 10" /> </param> <param name="jctside" type="integer" value="70" label="Junction side length threshold (default 70)"> <validator type="empty_field" message="You must enter a value, for the default value enter 70" /> </param> <param name="jctdistance" type="integer" value="200" label="Distance tolerance for junction compatibility (default 200)"> <validator type="empty_field" message="You must enter a value, for the default value enter 200" /> </param> <param name="jctlength" type="integer" value="500" label="Length threshold for compatible junctions (default 500)"> <validator type="empty_field" message="You must enter a value, for the default value enter 500" /> </param> <!--form field to select junction confidence in tumors--> <param name="jctpriority" type="select" label="Use normal junction priority for vcf output?"> <option value="" selected="true">no</option> <option value="--jctpriority">yes</option> </param> <!--form field to select junction confidence in tumors--> <param name="jcttumor" type="select" label="Use high confidence junctions for tumors?"> <option value="" selected="true">no</option> <option value="--jcttumor">yes</option> </param> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="GT">GT - Genotype</option> <option value="FT">FT - Sample genotype filters</option> <option value="SVTYPE">SVTYPE - Type of structural variation</option> <option value="CGA_BF">CGA_BF - Frequency in set of baseline genomes</option> <option value="CGA_MEDEL">CGA_MEDEL - Mobile element deletion</option> <option value="MATEID">MATEID - ID of mate breakend</option> <option value="CGA_BNDG">CGA_BNDG - Transcript name and strand of genes containing breakend</option> <option value="CGA_BNDGO">CGA_BNDGO - Transcript name and strand of genes containing mate breakend</option> <option value="CGA_BNDP">CGA_BNDP - Precision of breakend</option> <option value="CGA_BNDMPC">CGA_BNDMPC - Mate pair count supporting a breakend</option> <option value="CGA_BNDPOS">CGA_BNDPOS - Position of breakend as detected in individual genome</option> <option value="CGA_BNDDEF">CGA_BNDDEF - Breakend definition in individual genome</option> </param> </when> </conditional> </when> <when value="3"> <!--form field to select input sources--> <conditional name="sources"> <param name="source" type="select" label="Data sources to be included for each genome"> <option value="masterVar,CNV" selected="true">masterVar + CNV</option> <option value="masterVar">masterVar</option> <option value="CNV">CNV</option> </param> <when value="masterVar,CNV"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="out" selected="true">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="out"> <!--form field to select outside list of genome directories or mastervar files--> <param name="input" type="text" label="File with list of genome root directories" size="200" help="Enter file name with full path (/path/file). This file should contain a list of genome root directory names, one per line in the format /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01)."> <validator type="empty_field" message="You must supply the list of genome root directories"/> </param> </when> </conditional> <!--form field to select no-calls--> <param name="nocalls" type="select" label="Include no-calls?"> <option value="" selected="true">no</option> <option value="--nocalls">yes</option> </param> <!--form field to enter calibration directory--> <param name="calibration" type="text" size="300" label="Directory calibration data (/path/calibration-root)" help="The directory containing calibration data. For example, there should exist a file calibration-root/0.0.0/metrics.tsv. Calibration data can be downloaded from ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz"/> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="NS">NS - Number of samples</option> <option value="AN">AN - Total number of alleles in called genotypes</option> <option value="AC">AC - Allele count in genotypes</option> <option value="CGA_XR">CGA_XR - External database reference</option> <option value="CGA_FI">CGA_FI - Functional impact</option> <option value="CGA_PFAM">CGA_PFAM - PFAM domain </option> <option value="CGA_MIRB">CGA_MIRB - miRBaseId</option> <option value="CGA_SDO">CGA_SDO - Depth of overlapping segmental duplications</option> <option value="CGA_RPT">CGA_RPT - Overlapping repeatMasker annotations</option> <option value="GT">GT - Genotype</option> <option value="PS">PS - Phase set</option> <option value="FT">FT - Sample genotype filters</option> <option value="GL">GL - Genotype likelihoods</option> <option value="CGA_CEHQ">CGA_CEHQ - Calibrated haplotype quality based on EAF assumption</option> <option value="CGA_CEGL">CGA_CEGL - Genotype likelihoods based on CEHQ</option> <option value="SS">SS - Somatic status</option> <option value="HQ">HQ - Haplotype quality</option> <option value="EHQ">EHQ - Haplotype quality based on EAF assumption</option> <option value="GQ">GQ - Genotype quality</option> <option value="DP">DP - Total read depth</option> <option value="AD">AD - Allelic depths</option> <option value="CGA_RDP">CGA_RDP - Read depth in reference</option> <option value="CGA_ODP">CGA_ODP - Other total read depth: somatic comparison</option> <option value="CGA_OAD">CGA_OAD - Other allelic depths: somatic comparison</option> <option value="CGA_ORDP">CGA_ORDP - Other reference depth: somatic comparison </option> <option value="CGA_SOMC">CGA_SOMC - Somatic Category</option> <option value="CGA_SOMR">CGA_SOMR - Somatic Rank</option> <option value="CGA_SOMS">CGA_SOMS - Somatic Score</option> <option value="CGA_GP">CGA_GP - Normalized mean GC corrected coverage</option> <option value="CGA_NP">CGA_NP - Normalized mean coverage for 2k window</option> <option value="CGA_CP">CGA_CP - Diploid-model ploidy call for segment</option> <option value="CGA_PS">CGA_PS - Diploid-model called ploidy score</option> <option value="CGA_CT">CGA_CT - Diploid-model CNV type</option> <option value="CGA_TS">CGA_TS - Diploid-model CNV type score</option> <option value="CGA_CL">CGA_CL - Nondiploid-model called level</option> <option value="CGA_LS">CGA_LS - Nondiploid-model called level score</option> <option value="CGA_SCL">CGA_SCL - Nondiploid-model somatic called level</option> <option value="CGA_SLS">CGA_SLS - Non-diploid-model somatic called level score</option> <option value="CGA_LAF">CGA_LAF - Lesser Allele Fraction estimate, 100k window</option> <option value="CGA_LLAF">CGA_LLAF - Lesser Allele Fraction lower bound, 100k window</option> <option value="CGA_ULAF">CGA_ULAF - Lesser Allele Fraction upper bound, 100k window</option> </param> </when> <when value="masterVar"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="in" selected="true">imported into Galaxy</option> <option value="out">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="in"> <!--form field to select mastervar files--> <repeat name="files" title="MasterVar files" min="1"> <param name="input" type="data" format="cg_mastervar" label="Dataset"> <validator type="dataset_ok_validator" /> <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" metadata_name="dbkey" metadata_column="1" message="cgatools is not currently available for this build."/> </param> </repeat> </when> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="File with list of genome root directories or masterVar files" size="200" help="Enter file name with full path (/path/file). This file should contain a list of genome root directory names, one per line in the format /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01), or a list of masterVar files, one per line in the format /path/masterVarfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01/ASM/masterVarBeta-GS00000YYYY-ASM.tsv.bz2)."> <validator type="empty_field" message="You must supply the list of genome root directories or masterVar files"/> </param> </when> </conditional> <!--form field to select no-calls--> <param name="nocalls" type="select" label="Include no-calls?"> <option value="" selected="true">no</option> <option value="--nocalls">yes</option> </param> <!--form field to enter calibration directory--> <param name="calibration" type="text" size="300" label="Directory calibration data (/path/calibration-root)" help="The directory containing calibration data. For example, there should exist a file calibration-root/0.0.0/metrics.tsv. Calibration data can be downloaded from ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz"/> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="NS">NS - Number of samples</option> <option value="AN">AN - Total number of alleles in called genotypes</option> <option value="AC">AC - Allele count in genotypes</option> <option value="CGA_XR">CGA_XR - External database reference</option> <option value="CGA_FI">CGA_FI - Functional impact</option> <option value="CGA_PFAM">CGA_PFAM - PFAM domain </option> <option value="CGA_MIRB">CGA_MIRB - miRBaseId</option> <option value="CGA_SDO">CGA_SDO - Depth of overlapping segmental duplications</option> <option value="CGA_RPT">CGA_RPT - Overlapping repeatMasker annotations</option> <option value="GT">GT - Genotype</option> <option value="PS">PS - Phase set</option> <option value="FT">FT - Sample genotype filters</option> <option value="GL">GL - Genotype likelihoods</option> <option value="CGA_CEHQ">CGA_CEHQ - Calibrated haplotype quality based on EAF assumption</option> <option value="CGA_CEGL">CGA_CEGL - Genotype likelihoods based on CEHQ</option> <option value="SS">SS - Somatic status</option> <option value="HQ">HQ - Haplotype quality</option> <option value="EHQ">EHQ - Haplotype quality based on EAF assumption</option> <option value="GQ">GQ - Genotype quality</option> <option value="DP">DP - Total read depth</option> <option value="AD">AD - Allelic depths</option> <option value="CGA_RDP">CGA_RDP - Read depth in reference</option> <option value="CGA_ODP">CGA_ODP - Other total read depth: somatic comparison</option> <option value="CGA_OAD">CGA_OAD - Other allelic depths: somatic comparison</option> <option value="CGA_ORDP">CGA_ORDP - Other reference depth: somatic comparison </option> <option value="CGA_SOMC">CGA_SOMC - Somatic Category</option> <option value="CGA_SOMR">CGA_SOMR - Somatic Rank</option> <option value="CGA_SOMS">CGA_SOMS - Somatic Score</option> </param> </when> <when value="CNV"> <!--conditional to select inputs--> <conditional name="data_sources"> <param name="data_source" type="select" label="Where are the input files?"> <option value="out" selected="true">located outside Galaxy (data on server or mounted drive)</option> </param> <when value="out"> <!--form field to enter input file--> <param name="input" type="text" label="File with list of genome root directories" size="200" help="Enter file name with full path (/path/file). This file should contain a list of genome root directory names, one per line in the format /path/dir (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01)."> <validator type="empty_field" message="You must supply the list of genome root directories"/> </param> </when> </conditional> <!--form field to select field names to include in vcf--> <param name="fields" type="select" label="Field names to be included in vcf file" multiple="true" help="Select all field names (default) or a collection of individual field names."> <option value="all" selected="true">-- all (default) --</option> <option value="GT">GT - Genotype</option> <option value="CGA_GP">CGA_GP - Normalized mean GC corrected coverage</option> <option value="CGA_NP">CGA_NP - Normalized mean coverage for 2k window</option> <option value="CGA_CP">CGA_CP - Diploid-model ploidy call for segment</option> <option value="CGA_PS">CGA_PS - Diploid-model called ploidy score</option> <option value="CGA_CT">CGA_CT - Diploid-model CNV type</option> <option value="CGA_TS">CGA_TS - Diploid-model CNV type score</option> <option value="CGA_CL">CGA_CL - Nondiploid-model called level</option> <option value="CGA_LS">CGA_LS - Nondiploid-model called level score</option> <option value="CGA_SCL">CGA_SCL - Nondiploid-model somatic called level</option> <option value="CGA_SLS">CGA_SLS - Non-diploid-model somatic called level score</option> <option value="CGA_LAF">CGA_LAF - Lesser Allele Fraction estimate, 100k window</option> <option value="CGA_LLAF">CGA_LLAF - Lesser Allele Fraction lower bound, 100k window</option> <option value="CGA_ULAF">CGA_ULAF - Lesser Allele Fraction upper bound, 100k window</option> </param> </when> </conditional> </when> </conditional> </inputs> <help> **What it does** This tool uses cgatools mkvcf to convert Complete Genomics masterVar files, including CNV, SV and/or MEI data, to vcf format version. **cgatools 1.6.0 Documentation** Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf Release notes: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-release-notes.pdf **Command line reference**:: COMMAND NAME mkvcf - Converts var file(s) or masterVar file(s) to VCF. DESCRIPTION Converts var file(s) or masterVar file(s) to VCF. OPTIONS -h [ --help ] Print this help message. --beta This is a beta command. To run this command, you must pass the --beta flag. --reference arg The reference crr file. --output arg (=STDOUT) The output file (may be omitted for stdout). --field-names arg (=GT,PS,NS,AN,AC,SS,FT,CGA_XR,CGA_FI,GQ,HQ,EHQ,CGA_CEHQ,GL, CGA_CEGL,DP,AD,CGA_RDP,CGA_ODP,CGA_OAD,CGA_ORDP,CGA_PFAM,CGA_MIRB,CGA_RPT, CGA_SDO,CGA_SOMC,CGA_SOMR,CGA_SOMS,CGA_GP,CGA_NP,CGA_CP,CGA_PS,CGA_CT, CGA_TS,CGA_CL,CGA_LS,CGA_SCL,CGA_SLS,CGA_LAF,CGA_LLAF,CGA_ULAF,CGA_IS, CGA_IDC,CGA_IDCL,CGA_IDCR,CGA_RDC,CGA_NBET,CGA_ETS,CGA_KES,CGA_BF, CGA_MEDEL,MATEID,SVTYPE,CGA_BNDG,CGA_BNDGO,CGA_BNDMPC,CGA_BNDPOS,CGA_BNDDEF, CGA_BNDP) Comma-separated list of field names. By default, all fields are included, but you may override this option to ensure only a subset of the fields is included in the VCF output. For a description of each field, see the cgatools user guide. --source-names arg (=masterVar,CNV,SV,MEI) Comma-separated list of source names. The following source names are available: masterVar - Includes records extracted from the masterVar file. CNV - Includes CNV-related records. SV - Includes records derived from junctions files. MEI - Includes records describing mobile element insertions. Some of these source types are only available for more recent pipeline versions, and some of these source types do not support multi-genome VCFs. For more information about which source types are available for which versions of the Complete Genomics pipeline software, see the cgatools user guide. --genome-root arg For each genome to include in the VCF, the genome root directory, for example /data/GS00118-DNA_A01; this directory is expected to contain the ASM and LIB subdirectories, for example. You must supply this option for each genome in the VCF, unless you are using --source-names=masterVar and you have specified the --master-var option for each genome in the VCF. --master-var arg For each genome to include in the VCF, the masterVar file. If genome-roots parameter is given, this parameter defaults to the masterVar in the given genome-root. --include-no-calls Small variants VCF records include loci that have no reference-inconsistent calls. --calibration-root arg The directory containing calibration data. For example, there should exist a file calibration-root/version0.0.0/metrics.tsv. This option is only required if CGA_CEHQ or CGA_CEGL are included in the --field-names parameter. --junction-file arg For each genome to include in the VCF, the junctions file. If genome-roots parameter is given, this parameter defaults to the respective junctions file in the export directory. --junction-score-threshold arg (=10) Junction score thresholds (discordant mate pair count). --junction-side-length-threshold arg (=70) Junction side length threshold. --junction-distance-tolerance arg (=200) Distance tolerance for junction compatibility. --junction-length-threshold arg (=500) Length threshold for compatible junctions. --junction-normal-priority Normal junction priority for vcf output. --junction-tumor-hc use high confidence junctions for tumors. SUPPORTED FORMAT_VERSION 0.3 or later </help> </tool>