# HG changeset patch
# User recetox
# Date 1597413585 0
# Node ID 13bde05924da484d016394e203d5e9f8897272b4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"
diff -r 000000000000 -r 13bde05924da freebayes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/freebayes.xml Fri Aug 14 13:59:45 2020 +0000
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+
+ bayesian genetic variant detector
+
+ macros.xml
+
+
+ gawk
+ parallel
+
+ &1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
+ #else:
+ #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+ #end if
+
+ #if $reference_source.batchmode.processmode == 'merge':
+ #set $input_bamfiles = $reference_source.batchmode.input_bams
+ #else:
+ #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
+ #end if
+
+ #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
+ ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
+ ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
+ #end for
+
+ ## Tabixize optional input_variant_vcf file (for --variant-input option)
+ #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
+ ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
+ ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
+ #end if
+
+ ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
+ #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
+ ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
+ #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
+ printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
+ #else
+ ##divide up the regions in the bam file for efficient processing
+ #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
+ samtools view -H b_${bam_count}.bam |
+ grep '^@SQ' |
+ cut -f 2- |
+ awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
+ #end for
+ #end if
+
+ sort -u regions_all.bed > regions_uniq.bed &&
+ ## split into even small chunks, this has some disatvantages and will not be used for the moment
+ ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
+
+ mkdir vcf_output failed_alleles trace &&
+
+ ## Finished setting up inputs
+
+ for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
+ do
+ echo "
+
+ ## COMMAND LINE STARTS HERE
+
+ freebayes
+
+ --region '\$i'
+
+ #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
+ --bam 'b_${bam_count}.bam'
+ #end for
+ --fasta-reference '${reference_fasta_filename}'
+
+ ## Outputs
+ --vcf './vcf_output/part_\$i.vcf'
+
+ ## Coverage
+ #if str($coverage_options.coverage_options_selector) == "set":
+ @COVERAGE@
+ #end if
+
+ ##advanced options
+ #if str( $options_type.options_type_selector ) == "simple":
+ #pass
+ #elif str( $options_type.options_type_selector ) == "simple_w_filters":
+ --standard-filters
+ #elif str( $options_type.options_type_selector ) == "naive":
+ --haplotype-length 0
+ --min-alternate-count 1
+ --min-alternate-fraction 0.05
+ --pooled-continuous
+ --report-monomorphic
+ #elif str( $options_type.options_type_selector ) == "naive_w_filters":
+ --haplotype-length 0
+ --min-alternate-count 1
+ --min-alternate-fraction 0.05
+ --pooled-continuous
+ --report-monomorphic
+ --standard-filters
+ #elif str( $options_type.options_type_selector ) == "full":
+ #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
+ ${options_type.optional_inputs.report_monomorphic}
+
+ #if $options_type.optional_inputs.output_trace_option:
+ --trace ./trace/part_'\$i'.txt
+ #end if
+ #if $options_type.optional_inputs.output_failed_alleles_option:
+ --failed-alleles ./failed_alleles/part_'\$i'.bed
+ #end if
+ #if $options_type.optional_inputs.samples:
+ --samples '${options_type.optional_inputs.samples}'
+ #end if
+ #if $options_type.optional_inputs.populations:
+ --populations '${options_type.optional_inputs.populations}'
+ #end if
+ #if $options_type.optional_inputs.A:
+ --cnv-map '${options_type.optional_inputs.A}'
+ #end if
+ #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
+ --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above
+ ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
+ #end if
+ #if $options_type.optional_inputs.haplotype_basis_alleles:
+ --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
+ #end if
+ #if $options_type.optional_inputs.observation_bias:
+ --observation-bias '${options_type.optional_inputs.observation_bias}'
+ #end if
+ #if $options_type.optional_inputs.contamination_estimates:
+ --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
+ #end if
+ #end if
+
+ ## REPORTING
+ #if str( $options_type.reporting.reporting_selector ) == "set":
+ --pvar ${options_type.reporting.pvar}
+ #end if
+ ## POPULATION MODEL
+ #if str( $options_type.population_model.population_model_selector ) == "set":
+ --theta ${options_type.population_model.T}
+ --ploidy ${options_type.population_model.P}
+ ${options_type.population_model.J}
+ ${options_type.population_model.K}
+ #end if
+
+ ## REFERENCE ALLELE
+ #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
+ ${options_type.reference_allele.Z}
+ --reference-quality '${options_type.reference_allele.reference_quality}'
+ #end if
+
+ ## ALLELE SCOPE
+ #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
+ ${options_type.allele_scope.I}
+ ${options_type.allele_scope.i}
+ ${options_type.allele_scope.X}
+ ${options_type.allele_scope.u}
+ ${options_type.allele_scope.no_partial_observations}
+
+ -n ${options_type.allele_scope.n}
+
+ --haplotype-length ${options_type.allele_scope.haplotype_length}
+ --min-repeat-size ${options_type.allele_scope.min_repeat_length}
+ --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
+ #end if
+
+ ## REALIGNMENT
+ ${options_type.O}
+
+ ##INPUT FILTERS
+ #if str( $options_type.input_filters.input_filters_selector ) == "set":
+ ${options_type.input_filters.use_duplicate_reads}
+ -m ${options_type.input_filters.m}
+ -q ${options_type.input_filters.q}
+ -R ${options_type.input_filters.R}
+ -Y ${options_type.input_filters.Y}
+ -e ${options_type.input_filters.e}
+ -F ${options_type.input_filters.F}
+ -C ${options_type.input_filters.C}
+ -G ${options_type.input_filters.G}
+
+ #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
+ -Q ${options_type.input_filters.mismatch_filters.Q}
+ #if str($options_type.input_filters.mismatch_filters.U)
+ -U ${options_type.input_filters.mismatch_filters.U}
+ #end if
+ -z ${options_type.input_filters.mismatch_filters.z}
+
+ --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
+ #end if
+
+ --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
+ #end if
+
+ ## POPULATION AND MAPPABILITY PRIORS
+ #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
+ ${options_type.population_mappability_priors.k}
+ ${options_type.population_mappability_priors.w}
+ ${options_type.population_mappability_priors.V}
+ ${options_type.population_mappability_priors.a}
+ #end if
+
+ ## GENOTYPE LIKELIHOODS
+ #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
+ ${$options_type.genotype_likelihoods.experimental_gls}
+
+ --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
+ --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
+ #end if
+
+ ## ALGORITHMIC FEATURES
+ #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
+ -B '${options_type.algorithmic_features.B}'
+ -W '${options_type.algorithmic_features.W}'
+ -D '${options_type.algorithmic_features.D}'
+
+ #if str($options_type.algorithmic_features.genotype_variant_threshold)
+ -S ${options_type.algorithmic_features.genotype_variant_threshold}
+ #end if
+
+ ${options_type.algorithmic_features.N}
+ ${options_type.algorithmic_features.j}
+ ${options_type.algorithmic_features.H}
+ ${options_type.algorithmic_features.genotype_qualities}
+ ${options_type.algorithmic_features.report_genotype_likelihood_max}
+
+ --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
+ #end if
+ #end if
+
+ ";
+ done > freebayes_commands.sh &&
+
+ cat freebayes_commands.sh |
+ parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
+
+ ## make VCF header
+ grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
+
+ for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
+ do
+ ## if this fails then it bails out the script
+ cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
+ ;
+ done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
+
+ #if str( $options_type.options_type_selector ) == "full":
+ #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
+ #if $options_type.optional_inputs.output_failed_alleles_option:
+ &&
+ for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
+ do
+ cat "./failed_alleles/part_\$i.bed"
+ ;
+ done > '${output_failed_alleles_bed}'
+ #end if
+
+ #if $options_type.optional_inputs.output_trace_option:
+ &&
+ for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
+ do
+ cat './trace/part_\$i.txt'
+ ;
+ done > '${output_trace}'
+ #end if
+ #end if
+ #end if
+ ]]>
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+ ( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True
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+
+ :- Limit analysis to the specified region, 0-base coordinates,
+ end_position not included (same as BED format).
+ Either '-' or '..' maybe used as a separator.
+ --samples FILE Limit analysis to samples listed (one per line) in the FILE.
+ By default FreeBayes will analyze all samples in its input
+ BAM files.
+ --populations FILE Each line of FILE should list a sample and a population which
+ it is part of. The population-based bayesian inference model
+ will then be partitioned on the basis of the populations.
+ --cnv-map FILE Read a copy number map from the BED file FILE, which has
+ either a sample-level ploidy:
+ sample_name copy_number
+ or a region-specific format:
+ seq_name start end sample_name copy_number
+ ... for each region in each sample which does not have the
+ default copy number as set by --ploidy. These fields can be delimited
+ by space or tab.
+
+**Output**::
+
+ --vcf FILE Output VCF-format results to FILE. (default: stdout)
+ --gvcf Write gVCF output, which indicates coverage in uncalled regions.
+ --gvcf-chunk NUM When writing gVCF output emit a record for every NUM bases.
+ --gvcf-dont-use-chunk When writing the gVCF output emit a record for all bases if
+ set to "true" , will also route an int to --gvcf-chunk
+ similar to --output-mode EMIT_ALL_SITES from GATK
+ --variant-input VCF Use variants reported in VCF file as input to the algorithm.
+ Variants in this file will included in the output even if
+ there is not enough support in the data to pass input filters.
+ --only-use-input-alleles Only provide variant calls and genotype likelihoods for sites
+ and alleles which are provided in the VCF input, and provide
+ output in the VCF for all input alleles, not just those which
+ have support in the data.
+ --haplotype-basis-alleles VCF When specified, only variant alleles provided in this input
+ VCF will be used for the construction of complex or haplotype
+ alleles.
+ --report-all-haplotype-alleles At sites where genotypes are made over haplotype alleles,
+ provide information about all alleles in output, not only
+ those which are called.
+ --report-monomorphic Report even loci which appear to be monomorphic, and report all
+ considered alleles, even those which are not in called genotypes.
+ Loci which do not have any potential alternates have '.' for ALT.
+ --pvar N Report sites if the probability that there is a polymorphism
+ at the site is greater than N. default: 0.0. Note that post-
+ filtering is generally recommended over the use of this parameter.
+ --strict-vcf Generate strict VCF format (FORMAT/GQ will be an int)
+
+**Population model**::
+
+ --theta N The expected mutation rate or pairwise nucleotide diversity
+ among the population under analysis. This serves as the
+ single parameter to the Ewens Sampling Formula prior model
+ default: 0.001
+ --ploidy N Sets the default ploidy for the analysis to N. default: 2
+ --pooled-discrete Assume that samples result from pooled sequencing.
+ Model pooled samples using discrete genotypes across pools.
+ When using this flag, set --ploidy to the number of
+ alleles in each sample or use the --cnv-map to define
+ per-sample ploidy.
+ --pooled-continuous Output all alleles which pass input filters, regardles of
+ genotyping outcome or model.
+
+**Reference allele**::
+
+ --use-reference-allele This flag includes the reference allele in the analysis as
+ if it is another sample from the same population.
+ --reference-quality MQ,BQ Assign mapping quality of MQ to the reference allele at each
+ site and base quality of BQ. default: 100,60
+
+**Allele scope**::
+
+ --use-best-n-alleles N Evaluate only the best N SNP alleles, ranked by sum of
+ supporting quality scores. (Set to 0 to use all; default: all)
+ --max-complex-gap
+ --haplotype-length N Allow haplotype calls with contiguous embedded matches of up
+ to this length. Set N=-1 to disable clumping. (default: 3)
+ --min-repeat-size When assembling observations across repeats, require the total repeat
+ length at least this many bp. (default: 5)
+ --min-repeat-entropy N To detect interrupted repeats, build across sequence until it has
+ entropy > N bits per bp. Set to 0 to turn off. (default: 1)
+ --no-partial-observations Exclude observations which do not fully span the dynamically-determined
+ detection window. (default, use all observations, dividing partial
+ support across matching haplotypes when generating haplotypes.)
+
+**Indel realignment**::
+
+ --dont-left-align-indels Turn off left-alignment of indels, which is enabled by default.
+
+**Input filters**::
+
+ --use-duplicate-reads Include duplicate-marked alignments in the analysis.
+ default: exclude duplicates marked as such in alignments
+ --min-mapping-quality Q Exclude alignments from analysis if they have a mapping
+ quality less than Q. default: 1
+ --min-base-quality Q Exclude alleles from analysis if their supporting base
+ quality is less than Q. default: 0
+ --min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting
+ observations is at least Q. default: 0
+ --min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of
+ supporting reads is at least Q. default: 0
+ --mismatch-base-quality-threshold Q Count mismatches toward --read-mismatch-limit if the base
+ quality of the mismatch is >= Q. default: 10
+ --read-mismatch-limit N Exclude reads with more than N mismatches where each mismatch
+ has base quality >= mismatch-base-quality-threshold.
+ default: ~unbounded
+ --read-max-mismatch-fraction N Exclude reads with more than N [0,1] fraction of mismatches where
+ each mismatch has base quality >= mismatch-base-quality-threshold
+ default: 1.0
+ --read-snp-limit N Exclude reads with more than N base mismatches, ignoring gaps
+ with quality >= mismatch-base-quality-threshold.
+ default: ~unbounded
+ --read-indel-limit N Exclude reads with more than N separate gaps.
+ default: ~unbounded
+ --standard-filters Use stringent input base and mapping quality filters
+ Equivalent to -m 30 -q 20 -R 0 -S 0
+ --min-alternate-fraction N Require at least this fraction of observations supporting
+ an alternate allele within a single individual in the
+ in order to evaluate the position. default: 0.05
+ --min-alternate-count N Require at least this count of observations supporting
+ an alternate allele within a single individual in order
+ to evaluate the position. default: 2
+ --min-alternate-qsum N Require at least this sum of quality of observations supporting
+ an alternate allele within a single individual in order
+ to evaluate the position. default: 0
+ --min-alternate-total N Require at least this count of observations supporting
+ an alternate allele within the total population in order
+ to use the allele in analysis. default: 1
+ --min-coverage N Require at least this coverage to process a site. default: 0
+ --limit-coverage N Downsample per-sample coverage to this level if greater than this coverage.
+ default: no limit
+ --skip-coverage N Skip processing of alignments overlapping positions with coverage >N.
+ This filters sites above this coverage, but will also reduce data nearby.
+ default: no limit
+
+**Population priors**::
+
+ --no-population-priors Equivalent to --pooled-discrete --hwe-priors-off and removal of
+ Ewens Sampling Formula component of priors.
+
+**Mappability priors**::
+
+ --hwe-priors-off Disable estimation of the probability of the combination
+ arising under HWE given the allele frequency as estimated
+ by observation frequency.
+ --binomial-obs-priors-off Disable incorporation of prior expectations about observations.
+ Uses read placement probability, strand balance probability,
+ and read position (5'-3') probability.
+ --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles
+ as a component of the priors.
+
+**Genotype likelihoods**::
+
+ --observation-bias FILE Read length-dependent allele observation biases from FILE.
+ The format is [length] [alignment efficiency relative to reference]
+ where the efficiency is 1 if there is no relative observation bias.
+ --base-quality-cap Q Limit estimated observation quality by capping base quality at Q.
+ --prob-contamination F An estimate of contamination to use for all samples. default: 10e-9
+ --legacy-gls Use legacy (polybayes equivalent) genotype likelihood calculations
+ --contamination-estimates FILE A file containing per-sample estimates of contamination, such as
+ those generated by VerifyBamID. The format should be:
+ sample p(read=R|genotype=AR) p(read=A|genotype=AA)
+ Sample '*' can be used to set default contamination estimates.
+
+**Algorithmic features**::
+
+ --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided
+ from genotype likelihoods.
+ --genotyping-max-iterations N Iterate no more than N times during genotyping step. default: 1000.
+ --genotyping-max-banddepth N Integrate no deeper than the Nth best genotype by likelihood when
+ genotyping. default: 6.
+ --posterior-integration-limits N,M Integrate all genotype combinations in our posterior space
+ which include no more than N samples with their Mth best
+ data likelihood. default: 1,3.
+ --exclude-unobserved-genotypes Skip sample genotypings for which the sample has no supporting reads.
+ --genotype-variant-threshold N Limit posterior integration to samples where the second-best
+ genotype likelihood is no more than log(N) from the highest
+ genotype likelihood for the sample. default: ~unbounded
+ --use-mapping-quality Use mapping quality of alleles when calculating data likelihoods.
+ --harmonic-indel-quality Use a weighted sum of base qualities around an indel, scaled by the
+ distance from the indel. By default use a minimum BQ in flanking sequence.
+ --read-dependence-factor N Incorporate non-independence of reads by scaling successive
+ observations by this factor during data likelihood
+ calculations. default: 0.9
+ --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in
+ each sample field in the VCF output.
+
+------
+
+**Acknowledgments**
+
+The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
+TNG was developed by Bjoern Gruening.
+]]>
+
+
+
+ @article{Tange2011a,
+ title = {GNU Parallel - The Command-Line Power Tool},
+ author = {O. Tange},
+ address = {Frederiksberg, Denmark},
+ journal = {;login: The USENIX Magazine},
+ month = {Feb},
+ number = {1},
+ volume = {36},
+ url = {http://www.gnu.org/s/parallel},
+ year = {2011},
+ pages = {42-47}
+ }
+
+
+
diff -r 000000000000 -r 13bde05924da leftalign.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/leftalign.xml Fri Aug 14 13:59:45 2020 +0000
@@ -0,0 +1,70 @@
+
+
+ indels in BAM datasets
+
+ macros.xml
+
+
+ &1 || echo "Error running samtools faidx for leftalign" >&2 &&
+ #else:
+ #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+ #end if
+
+ ##start leftalign commandline
+ cat '${input_bam}' |
+ bamleftalign
+ --fasta-reference '${reference_fasta_filename}'
+ -c
+ --max-iterations "${iterations}"
+ > '${output_bam}'
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method is computationally inexpensive and handles the most common classes of alignment inconsistency.
+
+This is leftalign utility from FreeBayes package.
+
+
+
diff -r 000000000000 -r 13bde05924da macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Aug 14 13:59:45 2020 +0000
@@ -0,0 +1,56 @@
+
+ 1.3.1
+
+
+ freebayes
+ samtools
+
+
+
+
+
+
+ @misc{1207.3907,
+ Author = {Erik Garrison},
+ Title = {Haplotype-based variant detection from short-read sequencing},
+ Year = {2012},
+ Eprint = {arXiv:1207.3907},
+ url = {http://arxiv.org/abs/1207.3907}
+ }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ --min-coverage ${coverage_options.min_coverage}
+ --skip-coverage ${coverage_options.skip_coverage}
+ --limit-coverage ${coverage_options.limit_coverage}
+
+
+
+
+
+
+
diff -r 000000000000 -r 13bde05924da test-data/freebayes-hxb2-test5.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-hxb2-test5.vcf Fri Aug 14 13:59:45 2020 +0000
@@ -0,0 +1,74 @@
+##fileformat=VCFv4.2
+##fileDate=20191101
+##source=freeBayes v1.3.1-dirty
+##reference=localref.fa
+##contig=
+##phasing=none
+##commandline="freebayes --region K03455:0..9719 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_K03455:0..9719.vcf --min-coverage 250 --skip-coverage 0 --limit-coverage 0"
+##INFO=
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+##INFO=
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+##INFO=
+##INFO=
+##INFO=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881
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+K03455 2802 . C A 3.80909e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=672;DPB=672;DPRA=0;EPP=126.784;EPPR=65.6713;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=627.193;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1084;QR=20184;RO=613;RPL=56;RPP=118.251;RPPR=63.8009;RPR=1;RUN=1;SAF=56;SAP=118.251;SAR=1;SRF=403;SRP=134.96;SRR=210;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:672:613,57:613:20184:57:1084:0,-104.146,-1718.1
+K03455 2848 . TAAAAAAGAAAAAATC TAAAAAAAGAAAAAATC 18102 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=630;CIGAR=1M1I15M;DP=722;DPB=774.875;DPRA=0;EPP=43.2136;EPPR=13.8677;GTI=0;LEN=1;MEANALT=40;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=830.486;PAIRED=1;PAIREDR=1;PAO=22;PQA=531.5;PQR=553.5;PRO=23;QA=20369;QR=158;RO=5;RPL=282;RPP=18.0245;RPPR=3.44459;RPR=348;RUN=1;SAF=333;SAP=7.47733;SAR=297;SRF=3;SRP=3.44459;SRR=2;TYPE=ins;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:722:5,630:5:158:630:20369:-1818.16,-176.934,0
+K03455 2873 . AC AT 21993.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=754;CIGAR=1M1X;DP=773;DPB=775.5;DPRA=0;EPP=5.26817;EPPR=5.18177;GTI=0;LEN=1;MEANALT=5;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1039.03;PAIRED=1;PAIREDR=1;PAO=2.5;PQA=63;PQR=63;PRO=2.5;QA=24534;QR=37;RO=1;RPL=357;RPP=7.6182;RPPR=5.18177;RPR=397;RUN=1;SAF=378;SAP=3.02182;SAR=376;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:773:1,754:1:37:754:24534:-2203.73,-223.941,0
+K03455 2882 . G T 21924 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=721;CIGAR=1X;DP=736;DPB=736;DPRA=0;EPP=36.2149;EPPR=22.5536;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=945.018;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24583;QR=177;RO=9;RPL=353;RPP=3.68794;RPPR=9.04217;RPR=368;RUN=1;SAF=363;SAP=3.08559;SAR=358;SRF=7;SRP=9.04217;SRR=2;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:736:9,721:9:177:721:24583:-2195.37,-203.838,0
+K03455 2883 . GGT GGG 2.65192e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=46;CIGAR=2M1X;DP=726;DPB=731;DPRA=0;EPP=86.2815;EPPR=8.74455;GTI=0;LEN=1;MEANALT=6;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=660.068;PAIRED=1;PAIREDR=1;PAO=3.5;PQA=112;PQR=112;PRO=4.5;QA=1167;QR=22483;RO=668;RPL=43;RPP=78.5398;RPPR=3.12733;RPR=3;RUN=1;SAF=45;SAP=94.401;SAR=1;SRF=316;SRP=7.22322;SRR=352;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:726:668,46:668:22483:46:1167:0,-109.931,-1917.55
+K03455 2894 . T C 21733.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=717;CIGAR=1X;DP=723;DPB=723;DPRA=0;EPP=10.8876;EPPR=5.18177;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=991.951;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24231;QR=17;RO=1;RPL=373;RPP=5.55731;RPPR=5.18177;RPR=344;RUN=1;SAF=354;SAP=3.25561;SAR=363;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:723:1,717:1:17:717:24231:-2178.13,-214.613,0
+K03455 2906 . C T 20694.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=650;CIGAR=1X;DP=653;DPB=653;DPRA=0;EPP=3.86553;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=885.229;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23147;QR=65;RO=2;RPL=368;RPP=27.7183;RPPR=7.35324;RPR=282;RUN=1;SAF=301;SAP=10.7073;SAR=349;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:653:2,650:2:65:650:23147:-2076.11,-190.301,0
+K03455 2913 . G A 20816.6 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=638;CIGAR=1X;DP=639;DPB=639;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=878.93;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23329;QR=31;RO=1;RPL=402;RPP=96.7988;RPPR=5.18177;RPR=236;RUN=1;SAF=297;SAP=9.5996;SAR=341;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:639:1,638:1:31:638:23329:-2095.39,-189.259,0
diff -r 000000000000 -r 13bde05924da test-data/freebayes-hxb2-test6.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-hxb2-test6.vcf Fri Aug 14 13:59:45 2020 +0000
@@ -0,0 +1,83 @@
+##fileformat=VCFv4.2
+##fileDate=20191106
+##source=freeBayes v1.3.1-dirty
+##reference=localref.fa
+##contig=
+##phasing=none
+##commandline="freebayes --region K03455:0..9719 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_K03455:0..9719.vcf --min-coverage 0 --skip-coverage 0 --limit-coverage 400"
+##INFO=
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+K03455 2728 . T A 4.41787e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=25;CIGAR=1X;DP=459;DPB=459;DPRA=0;EPP=28.1125;EPPR=3.87378;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=475.527;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=444;QR=13384;RO=425;RPL=21;RPP=28.1125;RPPR=38.2086;RPR=4;RUN=1;SAF=25;SAP=57.2971;SAR=0;SRF=356;SRP=423.862;SRR=69;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:459:425,25:425:13384:25:444:0,-95.5268,-1164.2
+K03455 2797 . G A 20542.6 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=666;CIGAR=1X;DP=666;DPB=666;DPRA=0;EPP=133.429;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=927.877;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=23333;QR=0;RO=0;RPL=319;RPP=5.56651;RPPR=0;RPR=347;RUN=1;SAF=474;SAP=262.296;SAR=192;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:666:0,666:0:0:666:23333:-2098.99,-200.486,0
+K03455 2802 . C A 3.80909e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=672;DPB=672;DPRA=0;EPP=126.784;EPPR=65.6713;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=627.193;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1084;QR=20184;RO=613;RPL=56;RPP=118.251;RPPR=63.8009;RPR=1;RUN=1;SAF=56;SAP=118.251;SAR=1;SRF=403;SRP=134.96;SRR=210;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:672:613,57:613:20184:57:1084:0,-104.146,-1718.1
+K03455 2848 . TAAAAAAGAAAAAATC TAAAAAAAGAAAAAATC 18102 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=630;CIGAR=1M1I15M;DP=722;DPB=774.875;DPRA=0;EPP=43.2136;EPPR=13.8677;GTI=0;LEN=1;MEANALT=40;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=830.486;PAIRED=1;PAIREDR=1;PAO=22;PQA=531.5;PQR=553.5;PRO=23;QA=20369;QR=158;RO=5;RPL=282;RPP=18.0245;RPPR=3.44459;RPR=348;RUN=1;SAF=333;SAP=7.47733;SAR=297;SRF=3;SRP=3.44459;SRR=2;TYPE=ins;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:722:5,630:5:158:630:20369:-1818.16,-176.934,0
+K03455 2873 . AC AT 21993.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=754;CIGAR=1M1X;DP=773;DPB=775.5;DPRA=0;EPP=5.26817;EPPR=5.18177;GTI=0;LEN=1;MEANALT=5;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1039.03;PAIRED=1;PAIREDR=1;PAO=2.5;PQA=63;PQR=63;PRO=2.5;QA=24534;QR=37;RO=1;RPL=357;RPP=7.6182;RPPR=5.18177;RPR=397;RUN=1;SAF=378;SAP=3.02182;SAR=376;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:773:1,754:1:37:754:24534:-2203.73,-223.941,0
+K03455 2882 . G T 21924 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=721;CIGAR=1X;DP=736;DPB=736;DPRA=0;EPP=36.2149;EPPR=22.5536;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=945.018;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24583;QR=177;RO=9;RPL=353;RPP=3.68794;RPPR=9.04217;RPR=368;RUN=1;SAF=363;SAP=3.08559;SAR=358;SRF=7;SRP=9.04217;SRR=2;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:736:9,721:9:177:721:24583:-2195.37,-203.838,0
+K03455 2883 . GGT GGG 2.65192e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=46;CIGAR=2M1X;DP=726;DPB=731;DPRA=0;EPP=86.2815;EPPR=8.74455;GTI=0;LEN=1;MEANALT=6;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=660.068;PAIRED=1;PAIREDR=1;PAO=3.5;PQA=112;PQR=112;PRO=4.5;QA=1167;QR=22483;RO=668;RPL=43;RPP=78.5398;RPPR=3.12733;RPR=3;RUN=1;SAF=45;SAP=94.401;SAR=1;SRF=316;SRP=7.22322;SRR=352;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:726:668,46:668:22483:46:1167:0,-109.931,-1917.55
+K03455 2894 . T C 21733.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=717;CIGAR=1X;DP=723;DPB=723;DPRA=0;EPP=10.8876;EPPR=5.18177;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=991.951;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24231;QR=17;RO=1;RPL=373;RPP=5.55731;RPPR=5.18177;RPR=344;RUN=1;SAF=354;SAP=3.25561;SAR=363;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:723:1,717:1:17:717:24231:-2178.13,-214.613,0
+K03455 2906 . C T 20694.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=650;CIGAR=1X;DP=653;DPB=653;DPRA=0;EPP=3.86553;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=885.229;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23147;QR=65;RO=2;RPL=368;RPP=27.7183;RPPR=7.35324;RPR=282;RUN=1;SAF=301;SAP=10.7073;SAR=349;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:653:2,650:2:65:650:23147:-2076.11,-190.301,0
+K03455 2913 . G A 20816.6 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=638;CIGAR=1X;DP=639;DPB=639;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=878.93;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23329;QR=31;RO=1;RPL=402;RPP=96.7988;RPPR=5.18177;RPR=236;RUN=1;SAF=297;SAP=9.5996;SAR=341;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:639:1,638:1:31:638:23329:-2095.39,-189.259,0
+K03455 2987 . C T 6415.71 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=234;CIGAR=1X;DP=235;DPB=235;DPRA=0;EPP=16.4103;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=328.998;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7972;QR=0;RO=0;RPL=234;RPP=511.135;RPPR=0;RPR=0;RUN=1;SAF=98;SAP=16.4103;SAR=136;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:235:0,234:0:0:234:7972:-717.259,-70.441,0
+K03455 2992 . T G 2.14568e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=1X;DP=202;DPB=202;DPRA=0;EPP=26.8965;EPPR=8.54184;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=220.335;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=218;QR=6192;RO=190;RPL=11;RPP=26.8965;RPPR=415.59;RPR=0;RUN=1;SAF=11;SAP=26.8965;SAR=0;SRF=84;SRP=8.54184;SRR=106;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:202:190,11:190:6192:11:218:0,-40.8623,-537.516
+K03455 3016 . CACCA CACCG 2027.61 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=81;CIGAR=4M1X;DP=92;DPB=92.4;DPRA=0;EPP=25.5561;EPPR=0;GTI=0;LEN=1;MEANALT=6;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=86.0691;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2598;QR=0;RO=0;RPL=81;RPP=178.9;RPPR=0;RPR=0;RUN=1;SAF=55;SAP=25.5561;SAR=26;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:92:0,81:0:0:81:2598:-233.803,-24.3834,0
+K03455 3025 . T A 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=9.52472;EPPR=4.6389;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.9298;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=1423;RO=48;RPL=3;RPP=9.52472;RPPR=107.241;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=27;SRP=4.6389;SRR=21;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:51:48,3:48:1423:3:45:0,-11.1526,-124.109
+K03455 3035 . T A 2.21948e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=9.52472;EPPR=4.65535;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.669;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=54;QR=954;RO=33;RPL=3;RPP=9.52472;RPPR=74.6689;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=19;SRP=4.65535;SRR=14;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:37:33,3:33:954:3:54:0,-5.96965,-81.0818
+K03455 3036 . A G 1.09205e-09 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=9.52472;EPPR=26.2761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.1038;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=578;RO=21;RPL=3;RPP=9.52472;RPPR=48.6112;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=18;SRP=26.2761;SRR=3;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:24:21,3:21:578:3:67:0,-0.971771,-46.0254
+K03455 3042 . A C 7.93379e-05 . AB=0.25;ABP=9.52472;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=9.52472;EPPR=14.8328;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.9103;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=52;QR=233;RO=9;RPL=3;RPP=9.52472;RPPR=22.5536;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=8;SRP=14.8328;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:9,3:9:233:3:52:-1.24091,0,-17.6087
diff -r 000000000000 -r 13bde05924da test-data/freebayes-hxb2-test7.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-hxb2-test7.vcf Fri Aug 14 13:59:45 2020 +0000
@@ -0,0 +1,62 @@
+##fileformat=VCFv4.2
+##fileDate=20191030
+##source=freeBayes v1.3.1-dirty
+##reference=localref.fa
+##contig=
+##phasing=none
+##commandline="freebayes --region K03455:0..9719 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_K03455:0..9719.vcf --min-coverage 0 --skip-coverage 100 --limit-coverage 0"
+##INFO=
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+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881
diff -r 000000000000 -r 13bde05924da test-data/freebayes-hxb2.bam
Binary file test-data/freebayes-hxb2.bam has changed
diff -r 000000000000 -r 13bde05924da test-data/freebayes-hxb2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-hxb2.fasta Fri Aug 14 13:59:45 2020 +0000
@@ -0,0 +1,2 @@
+>K03455
+TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
diff -r 000000000000 -r 13bde05924da test-data/freebayes-phix174-test1.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-phix174-test1.vcf Fri Aug 14 13:59:45 2020 +0000
@@ -0,0 +1,93 @@
+##fileformat=VCFv4.2
+##fileDate=20191030
+##source=freeBayes v1.3.1-dirty
+##reference=localref.fa
+##contig=
+##phasing=none
+##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf"
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
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+##INFO=
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+##INFO=
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+##INFO=
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+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
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+##INFO=
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+##INFO=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
+phiX174 311 . A G 0.00392026 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=7.0097;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:478:2:70:-1.91487,0,-18.7749
+phiX174 374 . T G 23.3387 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=25;NS=1;NUMALT=1;ODDS=1.58025;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPL=1;RPP=3.0103;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:2,2:2:141:2:75:-5.19433,0,-3.54586
+phiX174 913 . A C 2.27318 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=29;NS=1;NUMALT=1;ODDS=0.380296;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=171;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:171:2:67:-3.54411,0,-6.47921
+phiX174 1205 . A C 0.00388031 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34;NS=1;NUMALT=1;ODDS=7.01995;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=7.35324;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:456:2:67:-2.11454,0,-21.3383
+phiX174 1245 . G T 0.0324554 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=28.4286;NS=1;NUMALT=1;ODDS=4.8927;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=389;RO=7;RPL=2;RPP=7.35324;RPPR=3.32051;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:389:2:70:-2.83427,0,-14.5618
+phiX174 1249 . T G 0.0166698 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=30.1429;NS=1;NUMALT=1;ODDS=5.56079;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=464;RO=7;RPL=1;RPP=3.0103;RPPR=5.80219;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:464:2:74:-1.94207,0,-16.5662
+phiX174 1445 . C A 0.147157 . AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=3.36782;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:5,2:5:273:2:76:-2.52649,0,-12.4911
+phiX174 1577 . A C 0.0123232 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=5.8634;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPL=1;RPP=3.0103;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:460:2:60:-1.81064,0,-19.8257
+phiX174 1631 . T G 0.00100612 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=8.3701;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:500:2:68:-1.52818,0,-17.3788
+phiX174 1665 . C A 0.0164128 . AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=37;MQMR=30.3333;NS=1;NUMALT=1;ODDS=5.57635;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=587;RO=9;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:9,2:9:587:2:65:-2.35331,0,-21.269
+phiX174 1772 . T G 0.0180574 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=5.48067;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:7,2:7:425:2:59:-1.97686,0,-17.3816
+phiX174 1786 . T G 7.94817e-05 . AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.9085;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=537;RO=10;RPL=0;RPP=7.35324;RPPR=6.48466;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=16.9077;SRR=9;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:10,2:10:537:2:59:-0.861483,0,-25.1364
+phiX174 1945 . T G 1.01422 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=1.3354;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:263:2:59:-3.25425,0,-11.8637
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+phiX174 2699 . C A 2.04855 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=0.517362;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:2,2:2:109:2:76:-3.4054,0,-5.58455
+phiX174 2722 . T G 1.01772 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=7.35324;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=1.33197;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:150:2:67:-3.1308,0,-7.62253
+phiX174 2814 . T G 0.670623 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=1.79322;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=135;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=9.52472;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:135:2:57:-2.93048,0,-6.73807
+phiX174 2828 . T G 0.160629 . AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31;NS=1;NUMALT=1;ODDS=3.27866;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=348;RO=6;RPL=0;RPP=7.35324;RPPR=4.45795;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:6,2:6:348:2:100:-3.34336,0,-13.6819
+phiX174 2983 . T G 1.55467 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=0.843116;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:150:2:57:-3.34311,0,-7.61298
+phiX174 3110 . T C 1.16857 . AB=0.333333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=1.17522;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPL=0;RPP=9.52472;RPPR=3.0103;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:6,3:6:361:3:94:-4.02963,0,-16.4039
+phiX174 3155 . T G 5.42491 . AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=0.911202;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:5,2:5:299:2:75:-4.38484,0,-11.5688
+phiX174 3184 . A C 0.000128182 . AB=0.153846;ABP=16.5402;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=3.0103;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.7273;NS=1;NUMALT=1;ODDS=10.4306;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=738;RO=11;RPL=1;RPP=3.0103;RPPR=4.78696;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=7.94546;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:13:11,2:11:738:2:75:-0.695464,0,-29.8019
+phiX174 3325 . A C 0.0705175 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=4.11232;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:284:2:58:-2.65031,0,-9.66348
+phiX174 3413 . T G 0.00284067 . AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31.6667;NS=1;NUMALT=1;ODDS=7.33194;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=537;RO=9;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=14.8328;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:9,2:9:537:2:57:-1.59087,0,-22.4183
+phiX174 3418 . A C 0.000937887 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=8.44033;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:526:2:60:-1.49768,0,-21.0207
+phiX174 3490 . A C 0.00226584 . AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=7.35324;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34.3333;NS=1;NUMALT=1;ODDS=7.5581;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=543;RO=9;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:9,2:9:543:2:66:-2.09471,0,-24.3433
+phiX174 3729 . C T 0.295112 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=2.65478;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=232;RO=4;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:232:2:63:-3.28331,0,-11.7007
+phiX174 4031 . T G 0.0784807 . AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=4.00441;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:6,2:6:322:2:85:-3.02817,0,-11.6802
+phiX174 4502 . A C 0.232919 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.89868;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPL=1;RPP=3.0103;RPPR=11.6962;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:284:2:55:-2.57533,0,-11.8832
+phiX174 4558 . C G 0.076247 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=4.03372;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:204:2:59:-2.68445,0,-8.4362
+phiX174 4655 . T G 0.399408 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.33999;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:193:2:70:-2.81796,0,-11.1489
+phiX174 4704 . T C 0.000171782 . AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=10.8276;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.1378;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=621;RO=10;RPL=0;RPP=7.35324;RPPR=3.87889;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=3.87889;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:10,2:10:621:2:58:-1.1962,0,-26.2058
diff -r 000000000000 -r 13bde05924da test-data/freebayes-phix174-test2.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-phix174-test2.vcf Fri Aug 14 13:59:45 2020 +0000
@@ -0,0 +1,80 @@
+##fileformat=VCFv4.2
+##fileDate=20191031
+##source=freeBayes v1.3.1-dirty
+##reference=localref.fa
+##contig=
+##phasing=none
+##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --min-coverage 14 --skip-coverage 0 --limit-coverage 0 --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic --standard-filters"
+##INFO=
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