Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools commit a35519a8cc09ea0a6e6ac5f57ff36fd738e5adb7 |
added:
extract_variants.xml test-data/input1.gvcf test-data/nonvariants_output1.vcf test-data/variants_noheader_output1.vcf test-data/variants_output1.vcf |
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diff -r 000000000000 -r bf8841b0a6b0 extract_variants.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_variants.xml Mon Feb 20 06:35:42 2017 -0500 |
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@@ -0,0 +1,79 @@ +<tool id="gvcftools_extract_variants" name="Extract Variants from gVCF files" version="0.1"> + <description>Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.</description> + + <requirements> + <requirement type="package" version="0.17.0">gvcftools</requirement> + </requirements> + + <command detect_errors="aggressive"> + <![CDATA[ + extract_variants + #if str( $advanced.advanced_options_selector ) == 'true': + '${advanced.skip_header}' '${advanced.invert}' + #end if + < '${gvcf_input}' > '${vcf_output}' + ]]>] + </command> + + <inputs> + <param name="gvcf_input" type="data" format="vcf" label="Variants (gVCF format)" /> + <conditional name="advanced"> + <param name="advanced_options_selector" type="select" label="Advanced options"> + <option value="true">Show advanced options</option> + <option value="false" selected="True">Don't show advanced options</option> + </param> + <when value="true"> + <param type="boolean" name="skip_header" argument="--skip-header" + truevalue="--skip-header" falsevalue="" + label="Write the variants output file without a header" /> + <param type="boolean" argument="--invert" + truevalue="--invert" falsevalue="" + label="Invert the filter so that only non-variant records are output" /> + </when> + <when value="false"></when> + </conditional> + </inputs> + + <outputs> + <data name="vcf_output" format="vcf" /> + </outputs> + + <tests> + <test> + <param name="gvcf_input" ftype="vcf" value="input1.gvcf" /> + <output name="vcf_output" ftype="vcf" value="variants_output1.vcf" /> + </test> + <test> + <param name="gvcf_input" ftype="vcf" value="input1.gvcf" /> + <param name="advanced_options_selector" value="true" /> + <param name="skip_header" value="True" /> + <output name="vcf_output" ftype="vcf" value="variants_noheader_output1.vcf" /> + </test> + <test> + <param name="gvcf_input" ftype="vcf" value="input1.gvcf" /> + <param name="advanced_options_selector" value="true" /> + <param name="invert" value="True" /> + <output name="vcf_output" ftype="vcf" value="nonvariants_output1.vcf" /> + </test> + + </tests> + + <help> + <![CDATA[ + Extract variants from a gVCF field, removing all non-variant blocks to yield a smaller variant only VCF file. + + From the `gvcftools`_ toolkit. + + .. _gvcftools: https://sites.google.com/site/gvcftools/ + ]]> + </help> + <citations> + <citation type="bibtex"> + @unpublished{gvcftools, + author = {Illumina, Inc.}, + title = {gvcftools}, + url = {https://sites.google.com/site/gvcftools/} + } + </citation> + </citations> +</tool> |
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diff -r 000000000000 -r bf8841b0a6b0 test-data/input1.gvcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.gvcf Mon Feb 20 06:35:42 2017 -0500 |
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b'@@ -0,0 +1,1000 @@\n+##fileformat=VCFv4.1\n+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n+##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:04:37 SAST 2015",Epoch=1433667877260,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2117_866#L5-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false G'..b'7\n+gi|448814763|ref|NC_000962.3|\t338185\t.\tC\t<NON_REF>\t.\t.\tEND=338185\tGT:DP:GQ:MIN_DP:PL\t0:1:40:1:0,41\n+gi|448814763|ref|NC_000962.3|\t338186\t.\tG\t<NON_REF>\t.\t.\tEND=338186\tGT:DP:GQ:MIN_DP:PL\t0:1:41:1:0,42\n+gi|448814763|ref|NC_000962.3|\t338187\t.\tT\t<NON_REF>\t.\t.\tEND=338187\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338188\t.\tT\t<NON_REF>\t.\t.\tEND=338188\tGT:DP:GQ:MIN_DP:PL\t0:1:33:1:0,34\n+gi|448814763|ref|NC_000962.3|\t338189\t.\tG\t<NON_REF>\t.\t.\tEND=338189\tGT:DP:GQ:MIN_DP:PL\t0:1:40:1:0,41\n+gi|448814763|ref|NC_000962.3|\t338190\t.\tA\t<NON_REF>\t.\t.\tEND=338190\tGT:DP:GQ:MIN_DP:PL\t0:1:37:1:0,38\n+gi|448814763|ref|NC_000962.3|\t338191\t.\tT\t<NON_REF>\t.\t.\tEND=338192\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338193\t.\tA\t<NON_REF>\t.\t.\tEND=338193\tGT:DP:GQ:MIN_DP:PL\t0:1:38:1:0,39\n+gi|448814763|ref|NC_000962.3|\t338194\t.\tT\t<NON_REF>\t.\t.\tEND=338194\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338195\t.\tG\t<NON_REF>\t.\t.\tEND=338196\tGT:DP:GQ:MIN_DP:PL\t0:1:41:1:0,42\n+gi|448814763|ref|NC_000962.3|\t338197\t.\tT\t<NON_REF>\t.\t.\tEND=338197\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338198\t.\tC\t<NON_REF>\t.\t.\tEND=338199\tGT:DP:GQ:MIN_DP:PL\t0:1:41:1:0,42\n+gi|448814763|ref|NC_000962.3|\t338200\t.\tT\t<NON_REF>\t.\t.\tEND=338200\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338201\t.\tC\t<NON_REF>\t.\t.\tEND=338201\tGT:DP:GQ:MIN_DP:PL\t0:1:41:1:0,42\n+gi|448814763|ref|NC_000962.3|\t338202\t.\tC\t<NON_REF>\t.\t.\tEND=338202\tGT:DP:GQ:MIN_DP:PL\t0:1:40:1:0,41\n+gi|448814763|ref|NC_000962.3|\t338203\t.\tC\t<NON_REF>\t.\t.\tEND=338203\tGT:DP:GQ:MIN_DP:PL\t0:2:81:2:0,82\n+gi|448814763|ref|NC_000962.3|\t338204\t.\tG\t<NON_REF>\t.\t.\tEND=338204\tGT:DP:GQ:MIN_DP:PL\t0:2:77:2:0,78\n+gi|448814763|ref|NC_000962.3|\t338205\t.\tC\t<NON_REF>\t.\t.\tEND=338206\tGT:DP:GQ:MIN_DP:PL\t0:2:80:2:0,81\n+gi|448814763|ref|NC_000962.3|\t338207\t.\tA\t<NON_REF>\t.\t.\tEND=338207\tGT:DP:GQ:MIN_DP:PL\t0:2:77:2:0,78\n+gi|448814763|ref|NC_000962.3|\t338208\t.\tC\t<NON_REF>\t.\t.\tEND=338379\tGT:DP:GQ:MIN_DP:PL\t0:8:99:3:0,108\n+gi|448814763|ref|NC_000962.3|\t338380\t.\tC\t<NON_REF>\t.\t.\tEND=338388\tGT:DP:GQ:MIN_DP:PL\t0:4:89:4:0,90\n+gi|448814763|ref|NC_000962.3|\t338389\t.\tC\t<NON_REF>\t.\t.\tEND=338389\tGT:DP:GQ:MIN_DP:PL\t0:4:44:4:0,45\n+gi|448814763|ref|NC_000962.3|\t338390\t.\tC\t<NON_REF>\t.\t.\tEND=338396\tGT:DP:GQ:MIN_DP:PL\t0:3:89:3:0,90\n+gi|448814763|ref|NC_000962.3|\t338397\t.\tT\t<NON_REF>\t.\t.\tEND=338400\tGT:DP:GQ:MIN_DP:PL\t0:3:44:2:0,45\n+gi|448814763|ref|NC_000962.3|\t338401\t.\tC\t<NON_REF>\t.\t.\tEND=338401\tGT:DP:GQ:MIN_DP:PL\t0:2:3:2:0,3\n+gi|448814763|ref|NC_000962.3|\t338402\t.\tG\t<NON_REF>\t.\t.\tEND=338402\tGT:DP:GQ:MIN_DP:PL\t0:2:44:2:0,45\n+gi|448814763|ref|NC_000962.3|\t338403\t.\tA\t<NON_REF>\t.\t.\tEND=338406\tGT:DP:GQ:MIN_DP:PL\t0:3:89:3:0,90\n+gi|448814763|ref|NC_000962.3|\t338407\t.\tG\t<NON_REF>\t.\t.\tEND=338407\tGT:DP:GQ:MIN_DP:PL\t0:2:76:2:0,77\n+gi|448814763|ref|NC_000962.3|\t338408\t.\tC\t<NON_REF>\t.\t.\tEND=338408\tGT:DP:GQ:MIN_DP:PL\t0:2:3:2:0,3\n+gi|448814763|ref|NC_000962.3|\t338409\t.\tC\t<NON_REF>\t.\t.\tEND=338413\tGT:DP:GQ:MIN_DP:PL\t0:2:81:2:0,81\n+gi|448814763|ref|NC_000962.3|\t338414\t.\tG\t<NON_REF>\t.\t.\tEND=338414\tGT:DP:GQ:MIN_DP:PL\t0:2:78:2:0,79\n+gi|448814763|ref|NC_000962.3|\t338415\t.\tT\t<NON_REF>\t.\t.\tEND=338415\tGT:DP:GQ:MIN_DP:PL\t0:2:65:2:0,66\n+gi|448814763|ref|NC_000962.3|\t338416\t.\tT\t<NON_REF>\t.\t.\tEND=338416\tGT:DP:GQ:MIN_DP:PL\t0:2:73:2:0,74\n+gi|448814763|ref|NC_000962.3|\t338417\t.\tT\t<NON_REF>\t.\t.\tEND=338417\tGT:DP:GQ:MIN_DP:PL\t0:2:44:2:0,45\n+gi|448814763|ref|NC_000962.3|\t338418\t.\tC\t<NON_REF>\t.\t.\tEND=338422\tGT:DP:GQ:MIN_DP:PL\t0:2:0:2:0,0\n+gi|448814763|ref|NC_000962.3|\t338423\t.\tG\t<NON_REF>\t.\t.\tEND=338425\tGT:DP:GQ:MIN_DP:PL\t0:3:44:3:0,45\n+gi|448814763|ref|NC_000962.3|\t338426\t.\tC\t<NON_REF>\t.\t.\tEND=338426\tGT:DP:GQ:MIN_DP:PL\t0:4:89:4:0,90\n+gi|448814763|ref|NC_000962.3|\t338427\t.\tC\t<NON_REF>\t.\t.\tEND=338434\tGT:DP:GQ:MIN_DP:PL\t0:4:99:4:0,130\n+gi|448814763|ref|NC_000962.3|\t338435\t.\tG\t<NON_REF>\t.\t.\tEND=338435\tGT:DP:GQ:MIN_DP:PL\t0:4:41:4:0,41\n+gi|448814763|ref|NC_000962.3|\t338436\t.\tC\t<NON_REF>\t.\t.\tEND=338452\tGT:DP:GQ:MIN_DP:PL\t0:7:99:6:0,195\n' |
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diff -r 000000000000 -r bf8841b0a6b0 test-data/nonvariants_output1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nonvariants_output1.vcf Mon Feb 20 06:35:42 2017 -0500 |
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b'@@ -0,0 +1,884 @@\n+##fileformat=VCFv4.1\n+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n+##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:04:37 SAST 2015",Epoch=1433667877260,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2117_866#L5-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false GV'..b'7\n+gi|448814763|ref|NC_000962.3|\t338185\t.\tC\t<NON_REF>\t.\t.\tEND=338185\tGT:DP:GQ:MIN_DP:PL\t0:1:40:1:0,41\n+gi|448814763|ref|NC_000962.3|\t338186\t.\tG\t<NON_REF>\t.\t.\tEND=338186\tGT:DP:GQ:MIN_DP:PL\t0:1:41:1:0,42\n+gi|448814763|ref|NC_000962.3|\t338187\t.\tT\t<NON_REF>\t.\t.\tEND=338187\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338188\t.\tT\t<NON_REF>\t.\t.\tEND=338188\tGT:DP:GQ:MIN_DP:PL\t0:1:33:1:0,34\n+gi|448814763|ref|NC_000962.3|\t338189\t.\tG\t<NON_REF>\t.\t.\tEND=338189\tGT:DP:GQ:MIN_DP:PL\t0:1:40:1:0,41\n+gi|448814763|ref|NC_000962.3|\t338190\t.\tA\t<NON_REF>\t.\t.\tEND=338190\tGT:DP:GQ:MIN_DP:PL\t0:1:37:1:0,38\n+gi|448814763|ref|NC_000962.3|\t338191\t.\tT\t<NON_REF>\t.\t.\tEND=338192\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338193\t.\tA\t<NON_REF>\t.\t.\tEND=338193\tGT:DP:GQ:MIN_DP:PL\t0:1:38:1:0,39\n+gi|448814763|ref|NC_000962.3|\t338194\t.\tT\t<NON_REF>\t.\t.\tEND=338194\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338195\t.\tG\t<NON_REF>\t.\t.\tEND=338196\tGT:DP:GQ:MIN_DP:PL\t0:1:41:1:0,42\n+gi|448814763|ref|NC_000962.3|\t338197\t.\tT\t<NON_REF>\t.\t.\tEND=338197\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338198\t.\tC\t<NON_REF>\t.\t.\tEND=338199\tGT:DP:GQ:MIN_DP:PL\t0:1:41:1:0,42\n+gi|448814763|ref|NC_000962.3|\t338200\t.\tT\t<NON_REF>\t.\t.\tEND=338200\tGT:DP:GQ:MIN_DP:PL\t0:1:35:1:0,36\n+gi|448814763|ref|NC_000962.3|\t338201\t.\tC\t<NON_REF>\t.\t.\tEND=338201\tGT:DP:GQ:MIN_DP:PL\t0:1:41:1:0,42\n+gi|448814763|ref|NC_000962.3|\t338202\t.\tC\t<NON_REF>\t.\t.\tEND=338202\tGT:DP:GQ:MIN_DP:PL\t0:1:40:1:0,41\n+gi|448814763|ref|NC_000962.3|\t338203\t.\tC\t<NON_REF>\t.\t.\tEND=338203\tGT:DP:GQ:MIN_DP:PL\t0:2:81:2:0,82\n+gi|448814763|ref|NC_000962.3|\t338204\t.\tG\t<NON_REF>\t.\t.\tEND=338204\tGT:DP:GQ:MIN_DP:PL\t0:2:77:2:0,78\n+gi|448814763|ref|NC_000962.3|\t338205\t.\tC\t<NON_REF>\t.\t.\tEND=338206\tGT:DP:GQ:MIN_DP:PL\t0:2:80:2:0,81\n+gi|448814763|ref|NC_000962.3|\t338207\t.\tA\t<NON_REF>\t.\t.\tEND=338207\tGT:DP:GQ:MIN_DP:PL\t0:2:77:2:0,78\n+gi|448814763|ref|NC_000962.3|\t338208\t.\tC\t<NON_REF>\t.\t.\tEND=338379\tGT:DP:GQ:MIN_DP:PL\t0:8:99:3:0,108\n+gi|448814763|ref|NC_000962.3|\t338380\t.\tC\t<NON_REF>\t.\t.\tEND=338388\tGT:DP:GQ:MIN_DP:PL\t0:4:89:4:0,90\n+gi|448814763|ref|NC_000962.3|\t338389\t.\tC\t<NON_REF>\t.\t.\tEND=338389\tGT:DP:GQ:MIN_DP:PL\t0:4:44:4:0,45\n+gi|448814763|ref|NC_000962.3|\t338390\t.\tC\t<NON_REF>\t.\t.\tEND=338396\tGT:DP:GQ:MIN_DP:PL\t0:3:89:3:0,90\n+gi|448814763|ref|NC_000962.3|\t338397\t.\tT\t<NON_REF>\t.\t.\tEND=338400\tGT:DP:GQ:MIN_DP:PL\t0:3:44:2:0,45\n+gi|448814763|ref|NC_000962.3|\t338401\t.\tC\t<NON_REF>\t.\t.\tEND=338401\tGT:DP:GQ:MIN_DP:PL\t0:2:3:2:0,3\n+gi|448814763|ref|NC_000962.3|\t338402\t.\tG\t<NON_REF>\t.\t.\tEND=338402\tGT:DP:GQ:MIN_DP:PL\t0:2:44:2:0,45\n+gi|448814763|ref|NC_000962.3|\t338403\t.\tA\t<NON_REF>\t.\t.\tEND=338406\tGT:DP:GQ:MIN_DP:PL\t0:3:89:3:0,90\n+gi|448814763|ref|NC_000962.3|\t338407\t.\tG\t<NON_REF>\t.\t.\tEND=338407\tGT:DP:GQ:MIN_DP:PL\t0:2:76:2:0,77\n+gi|448814763|ref|NC_000962.3|\t338408\t.\tC\t<NON_REF>\t.\t.\tEND=338408\tGT:DP:GQ:MIN_DP:PL\t0:2:3:2:0,3\n+gi|448814763|ref|NC_000962.3|\t338409\t.\tC\t<NON_REF>\t.\t.\tEND=338413\tGT:DP:GQ:MIN_DP:PL\t0:2:81:2:0,81\n+gi|448814763|ref|NC_000962.3|\t338414\t.\tG\t<NON_REF>\t.\t.\tEND=338414\tGT:DP:GQ:MIN_DP:PL\t0:2:78:2:0,79\n+gi|448814763|ref|NC_000962.3|\t338415\t.\tT\t<NON_REF>\t.\t.\tEND=338415\tGT:DP:GQ:MIN_DP:PL\t0:2:65:2:0,66\n+gi|448814763|ref|NC_000962.3|\t338416\t.\tT\t<NON_REF>\t.\t.\tEND=338416\tGT:DP:GQ:MIN_DP:PL\t0:2:73:2:0,74\n+gi|448814763|ref|NC_000962.3|\t338417\t.\tT\t<NON_REF>\t.\t.\tEND=338417\tGT:DP:GQ:MIN_DP:PL\t0:2:44:2:0,45\n+gi|448814763|ref|NC_000962.3|\t338418\t.\tC\t<NON_REF>\t.\t.\tEND=338422\tGT:DP:GQ:MIN_DP:PL\t0:2:0:2:0,0\n+gi|448814763|ref|NC_000962.3|\t338423\t.\tG\t<NON_REF>\t.\t.\tEND=338425\tGT:DP:GQ:MIN_DP:PL\t0:3:44:3:0,45\n+gi|448814763|ref|NC_000962.3|\t338426\t.\tC\t<NON_REF>\t.\t.\tEND=338426\tGT:DP:GQ:MIN_DP:PL\t0:4:89:4:0,90\n+gi|448814763|ref|NC_000962.3|\t338427\t.\tC\t<NON_REF>\t.\t.\tEND=338434\tGT:DP:GQ:MIN_DP:PL\t0:4:99:4:0,130\n+gi|448814763|ref|NC_000962.3|\t338435\t.\tG\t<NON_REF>\t.\t.\tEND=338435\tGT:DP:GQ:MIN_DP:PL\t0:4:41:4:0,41\n+gi|448814763|ref|NC_000962.3|\t338436\t.\tC\t<NON_REF>\t.\t.\tEND=338452\tGT:DP:GQ:MIN_DP:PL\t0:7:99:6:0,195\n' |
b |
diff -r 000000000000 -r bf8841b0a6b0 test-data/variants_noheader_output1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants_noheader_output1.vcf Mon Feb 20 06:35:42 2017 -0500 |
b |
b'@@ -0,0 +1,116 @@\n+gi|448814763|ref|NC_000962.3|\t1977\t.\tA\tG,<NON_REF>\t1986\t.\tDP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,53,0:53:99:2016,0,2016:0,0,11,42\n+gi|448814763|ref|NC_000962.3|\t4013\t.\tT\tC,<NON_REF>\t2081\t.\tDP=53;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,53,0:53:99:2111,0,2111:0,0,29,24\n+gi|448814763|ref|NC_000962.3|\t7362\t.\tG\tC,<NON_REF>\t3369\t.\tBaseQRankSum=1.693;ClippingRankSum=1.693;DP=88;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=0.827;ReadPosRankSum=1.614\tGT:AD:DP:GQ:PL:SB\t1:1,87,0:88:99:3399,0,3408:0,1,40,47\n+gi|448814763|ref|NC_000962.3|\t7585\t.\tG\tC,<NON_REF>\t2294\t.\tDP=61;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,60,0:60:99:2324,0,2324:0,0,36,24\n+gi|448814763|ref|NC_000962.3|\t9304\t.\tG\tA,<NON_REF>\t2343\t.\tDP=69;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,69,0:69:99:2373,0,2373:0,0,31,38\n+gi|448814763|ref|NC_000962.3|\t11311\t.\tA\tC,<NON_REF>\t3627\t.\tDP=96;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,96,0:96:99:3657,0,3657:0,0,31,65\n+gi|448814763|ref|NC_000962.3|\t11370\t.\tC\tT,<NON_REF>\t2699\t.\tDP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,77,0:77:99:2729,0,2729:0,0,21,56\n+gi|448814763|ref|NC_000962.3|\t11879\t.\tA\tG,<NON_REF>\t2659\t.\tDP=70;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,69,0:69:99:2689,0,2689:0,0,36,33\n+gi|448814763|ref|NC_000962.3|\t14785\t.\tT\tC,<NON_REF>\t3506\t.\tDP=90;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,90,0:90:99:3536,0,3536:0,0,38,52\n+gi|448814763|ref|NC_000962.3|\t21795\t.\tG\tA,<NON_REF>\t784\t.\tDP=24;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,24,0:24:99:814,0,814:0,0,8,16\n+gi|448814763|ref|NC_000962.3|\t24698\t.\tGCCGCGTTGCTCGGGGTAA\tG,<NON_REF>\t1536.97\t.\tDP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.01;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,36,0:36:99:1576,0,1576:0,0,25,11\n+gi|448814763|ref|NC_000962.3|\t26959\t.\tC\tG,<NON_REF>\t2474\t.\tDP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,66,0:66:99:2504,0,2504:0,0,41,25\n+gi|448814763|ref|NC_000962.3|\t29482\t.\tCA\tC,<NON_REF>\t2528.97\t.\tDP=74;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.14;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,72,0:72:99:2568,0,2568:0,0,34,38\n+gi|448814763|ref|NC_000962.3|\t30519\t.\tC\tT,<NON_REF>\t2289\t.\tBaseQRankSum=1.681;ClippingRankSum=0.026;DP=68;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0;MQRankSum=-1.525;ReadPosRankSum=1.060\tGT:AD:DP:GQ:PL:SB\t1:1,66,0:67:99:2319,0,2329:1,0,47,19\n+gi|448814763|ref|NC_000962.3|\t30688\t.\tT\tG,<NON_REF>\t2109\t.\tDP=56;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,56,0:56:99:2139,0,2139:0,0,30,26\n+gi|448814763|ref|NC_000962.3|\t30943\t.\tC\tT,<NON_REF>\t1534\t.\tDP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,49,0:49:99:1564,0,1564:0,0,28,21\n+gi|448814763|ref|NC_000962.3|\t31077\t.\tC\tT,<NON_REF>\t1499\t.\tDP=43;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,43,0:43:99:1529,0,1529:0,0,24,19\n+gi|448814763|ref|NC_000962.3|\t32349\t.\tCCCGCGCGTCGGCGATGCGTCGCGTCGAGTCGGCGATG\tC,<NON_REF>\t3070.97\t.\tDP=75;MLEAC=1,0;MLEAF=1.00,0.00;MQ=65.20;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,70,0:70:99:3110,0,3110:0,0,35,35\n+gi|448814763|ref|NC_000962.3|\t34044\t.\tT\tC,<NON_REF>\t3703\t.\tDP=94;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,94,0:94:99:3733,0,3733:0,0,60,34\n+gi|448814763|ref|NC_000962.3|\t37031\t.\tC\tG,<NON_REF>\t1773\t.\tDP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,46,0:46:99:1803,0,1803:0,0,22,24\n+gi|448814763|ref|NC_000962.3|\t37910\t.\tC\tA,<NON_REF>\t3793\t.\tDP=113;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,113,0:113:99:3823,0,3823:0,0,62,51\n+gi|448814763|ref|NC_000962.3|\t39223\t.\tGC\tG,<NON_REF>\t1460.97\t.\tDP=50;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,46,0:46:99:1500,0,1500:0,0,19,27\n+gi|448814763|ref|NC_000962.3|\t42967\t.\tG\tC,<NON_REF>\t2609\t.\tDP=67;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,67,0:67:99:2639,0,2639:0,0,15,52\n+gi|448814763|ref|NC_000962.3|\t5055'..b'00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,31,0:31:99:1049,0,1049:0,0,22,9\n+gi|448814763|ref|NC_000962.3|\t285772\t.\tA\tC,<NON_REF>\t1085\t.\tDP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,28,0:28:99:1115,0,1115:0,0,11,17\n+gi|448814763|ref|NC_000962.3|\t285871\t.\tA\tG,<NON_REF>\t1112\t.\tDP=29;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,29,0:29:99:1142,0,1142:0,0,19,10\n+gi|448814763|ref|NC_000962.3|\t293628\t.\tA\tAC,<NON_REF>\t1458.97\t.\tDP=46;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,46,0:46:99:1498,0,1498:0,0,36,10\n+gi|448814763|ref|NC_000962.3|\t301290\t.\tG\tA,<NON_REF>\t2691\t.\tDP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,81,0:81:99:2721,0,2721:0,0,41,40\n+gi|448814763|ref|NC_000962.3|\t304679\t.\tG\tT,<NON_REF>\t3530\t.\tDP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,101,0:101:99:3560,0,3560:0,0,46,55\n+gi|448814763|ref|NC_000962.3|\t304923\t.\tA\tG,<NON_REF>\t3082\t.\tDP=84;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,84,0:84:99:3112,0,3112:0,0,52,32\n+gi|448814763|ref|NC_000962.3|\t310973\t.\tG\tA,<NON_REF>\t1535\t.\tDP=45;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,45,0:45:99:1565,0,1565:0,0,28,17\n+gi|448814763|ref|NC_000962.3|\t311613\t.\tG\tT,<NON_REF>\t2695\t.\tDP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,77,0:77:99:2725,0,2725:0,0,44,33\n+gi|448814763|ref|NC_000962.3|\t315502\t.\tC\tA,<NON_REF>\t1010\t.\tDP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,30,0:30:99:1040,0,1040:0,0,14,16\n+gi|448814763|ref|NC_000962.3|\t320038\t.\tG\tA,<NON_REF>\t626\t.\tDP=19;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,19,0:19:99:656,0,656:0,0,9,10\n+gi|448814763|ref|NC_000962.3|\t328641\t.\tG\tT,<NON_REF>\t1816\t.\tDP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,51,0:51:99:1846,0,1846:0,0,17,34\n+gi|448814763|ref|NC_000962.3|\t335971\t.\tA\tG,<NON_REF>\t1022\t.\tDP=25;MLEAC=1,0;MLEAF=1.00,0.00;MQ=63.45;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,25,0:25:99:1052,0,1052:0,0,12,13\n+gi|448814763|ref|NC_000962.3|\t336047\t.\tC\tG,<NON_REF>\t1353\t.\tBaseQRankSum=-0.603;ClippingRankSum=-1.789;DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.67;MQ0=0;MQRankSum=1.492;ReadPosRankSum=-2.141\tGT:AD:DP:GQ:PL:SB\t1:14,43,0:57:99:1383,0,2013:7,7,18,25\n+gi|448814763|ref|NC_000962.3|\t336050\t.\tA\tG,<NON_REF>\t1240\t.\tBaseQRankSum=3.331;ClippingRankSum=-0.852;DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.28;MQ0=0;MQRankSum=-0.808;ReadPosRankSum=-1.826\tGT:AD:DP:GQ:PL:SB\t1:14,35,0:49:99:1270,0,1900:7,7,12,23\n+gi|448814763|ref|NC_000962.3|\t336053\t.\tG\tC,<NON_REF>\t870\t.\tBaseQRankSum=-0.454;ClippingRankSum=-0.570;DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.16;MQ0=0;MQRankSum=0.896;ReadPosRankSum=-1.780\tGT:AD:DP:GQ:PL:SB\t1:14,33,0:47:99:900,0,1530:7,7,11,22\n+gi|448814763|ref|NC_000962.3|\t336191\t.\tC\tT,<NON_REF>\t1569\t.\tDP=44;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.79;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,44,0:44:99:1599,0,1599:0,0,38,6\n+gi|448814763|ref|NC_000962.3|\t336772\t.\tC\tT,<NON_REF>\t364\t.\tDP=9;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,9,0:9:99:394,0,394:0,0,1,8\n+gi|448814763|ref|NC_000962.3|\t336773\t.\tA\tG,<NON_REF>\t364\t.\tDP=8;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,8,0:8:99:394,0,394:0,0,1,7\n+gi|448814763|ref|NC_000962.3|\t336780\t.\tG\tA,<NON_REF>\t285\t.\tDP=4;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,4,0:4:99:315,0,315:0,0,0,4\n+gi|448814763|ref|NC_000962.3|\t336781\t.\tT\tC,<NON_REF>\t150\t.\tDP=3;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,3,0:3:99:180,0,180:0,0,0,3\n+gi|448814763|ref|NC_000962.3|\t336782\t.\tG\tC,<NON_REF>\t150\t.\tDP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,2,0:2:99:180,0,180:0,0,0,2\n+gi|448814763|ref|NC_000962.3|\t338020\t.\tA\tC,<NON_REF>\t45\t.\tDP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,2,0:2:75:75,0,75:0,0,2,0\n+gi|448814763|ref|NC_000962.3|\t338100\t.\tT\tC,<NON_REF>\t216\t.\tDP=6;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.19;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,6,0:6:99:246,0,246:0,0,6,0\n' |
b |
diff -r 000000000000 -r bf8841b0a6b0 test-data/variants_output1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants_output1.vcf Mon Feb 20 06:35:42 2017 -0500 |
[ |
b'@@ -0,0 +1,208 @@\n+##fileformat=VCFv4.1\n+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n+##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:04:37 SAST 2015",Epoch=1433667877260,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2117_866#L5-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false GV'..b'00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,31,0:31:99:1049,0,1049:0,0,22,9\n+gi|448814763|ref|NC_000962.3|\t285772\t.\tA\tC,<NON_REF>\t1085\t.\tDP=28;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,28,0:28:99:1115,0,1115:0,0,11,17\n+gi|448814763|ref|NC_000962.3|\t285871\t.\tA\tG,<NON_REF>\t1112\t.\tDP=29;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,29,0:29:99:1142,0,1142:0,0,19,10\n+gi|448814763|ref|NC_000962.3|\t293628\t.\tA\tAC,<NON_REF>\t1458.97\t.\tDP=46;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,46,0:46:99:1498,0,1498:0,0,36,10\n+gi|448814763|ref|NC_000962.3|\t301290\t.\tG\tA,<NON_REF>\t2691\t.\tDP=81;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,81,0:81:99:2721,0,2721:0,0,41,40\n+gi|448814763|ref|NC_000962.3|\t304679\t.\tG\tT,<NON_REF>\t3530\t.\tDP=101;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,101,0:101:99:3560,0,3560:0,0,46,55\n+gi|448814763|ref|NC_000962.3|\t304923\t.\tA\tG,<NON_REF>\t3082\t.\tDP=84;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,84,0:84:99:3112,0,3112:0,0,52,32\n+gi|448814763|ref|NC_000962.3|\t310973\t.\tG\tA,<NON_REF>\t1535\t.\tDP=45;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,45,0:45:99:1565,0,1565:0,0,28,17\n+gi|448814763|ref|NC_000962.3|\t311613\t.\tG\tT,<NON_REF>\t2695\t.\tDP=77;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,77,0:77:99:2725,0,2725:0,0,44,33\n+gi|448814763|ref|NC_000962.3|\t315502\t.\tC\tA,<NON_REF>\t1010\t.\tDP=30;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,30,0:30:99:1040,0,1040:0,0,14,16\n+gi|448814763|ref|NC_000962.3|\t320038\t.\tG\tA,<NON_REF>\t626\t.\tDP=19;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,19,0:19:99:656,0,656:0,0,9,10\n+gi|448814763|ref|NC_000962.3|\t328641\t.\tG\tT,<NON_REF>\t1816\t.\tDP=51;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,51,0:51:99:1846,0,1846:0,0,17,34\n+gi|448814763|ref|NC_000962.3|\t335971\t.\tA\tG,<NON_REF>\t1022\t.\tDP=25;MLEAC=1,0;MLEAF=1.00,0.00;MQ=63.45;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,25,0:25:99:1052,0,1052:0,0,12,13\n+gi|448814763|ref|NC_000962.3|\t336047\t.\tC\tG,<NON_REF>\t1353\t.\tBaseQRankSum=-0.603;ClippingRankSum=-1.789;DP=57;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.67;MQ0=0;MQRankSum=1.492;ReadPosRankSum=-2.141\tGT:AD:DP:GQ:PL:SB\t1:14,43,0:57:99:1383,0,2013:7,7,18,25\n+gi|448814763|ref|NC_000962.3|\t336050\t.\tA\tG,<NON_REF>\t1240\t.\tBaseQRankSum=3.331;ClippingRankSum=-0.852;DP=49;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.28;MQ0=0;MQRankSum=-0.808;ReadPosRankSum=-1.826\tGT:AD:DP:GQ:PL:SB\t1:14,35,0:49:99:1270,0,1900:7,7,12,23\n+gi|448814763|ref|NC_000962.3|\t336053\t.\tG\tC,<NON_REF>\t870\t.\tBaseQRankSum=-0.454;ClippingRankSum=-0.570;DP=47;MLEAC=1,0;MLEAF=1.00,0.00;MQ=67.16;MQ0=0;MQRankSum=0.896;ReadPosRankSum=-1.780\tGT:AD:DP:GQ:PL:SB\t1:14,33,0:47:99:900,0,1530:7,7,11,22\n+gi|448814763|ref|NC_000962.3|\t336191\t.\tC\tT,<NON_REF>\t1569\t.\tDP=44;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.79;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,44,0:44:99:1599,0,1599:0,0,38,6\n+gi|448814763|ref|NC_000962.3|\t336772\t.\tC\tT,<NON_REF>\t364\t.\tDP=9;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,9,0:9:99:394,0,394:0,0,1,8\n+gi|448814763|ref|NC_000962.3|\t336773\t.\tA\tG,<NON_REF>\t364\t.\tDP=8;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,8,0:8:99:394,0,394:0,0,1,7\n+gi|448814763|ref|NC_000962.3|\t336780\t.\tG\tA,<NON_REF>\t285\t.\tDP=4;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,4,0:4:99:315,0,315:0,0,0,4\n+gi|448814763|ref|NC_000962.3|\t336781\t.\tT\tC,<NON_REF>\t150\t.\tDP=3;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,3,0:3:99:180,0,180:0,0,0,3\n+gi|448814763|ref|NC_000962.3|\t336782\t.\tG\tC,<NON_REF>\t150\t.\tDP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,2,0:2:99:180,0,180:0,0,0,2\n+gi|448814763|ref|NC_000962.3|\t338020\t.\tA\tC,<NON_REF>\t45\t.\tDP=2;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,2,0:2:75:75,0,75:0,0,2,0\n+gi|448814763|ref|NC_000962.3|\t338100\t.\tT\tC,<NON_REF>\t216\t.\tDP=6;MLEAC=1,0;MLEAF=1.00,0.00;MQ=69.19;MQ0=0\tGT:AD:DP:GQ:PL:SB\t1:0,6,0:6:99:246,0,246:0,0,6,0\n' |