bio-vcf 0.8.2 → 0.9.0

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Files changed (62) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +8 -2
  3. data/Gemfile +4 -6
  4. data/README.md +92 -57
  5. data/Rakefile +3 -41
  6. data/TAGS +115 -0
  7. data/VERSION +1 -1
  8. data/bin/bio-vcf +58 -70
  9. data/bio-vcf.gemspec +23 -75
  10. data/features/cli.feature +6 -1
  11. data/features/multisample.feature +12 -0
  12. data/features/step_definitions/cli-feature.rb +2 -2
  13. data/features/step_definitions/multisample.rb +19 -0
  14. data/features/step_definitions/vcf_header.rb +1 -1
  15. data/features/support/env.rb +0 -9
  16. data/lib/bio-vcf/pcows.rb +210 -0
  17. data/lib/bio-vcf/vcfheader.rb +28 -9
  18. data/lib/bio-vcf/vcfheader_line.rb +455 -160
  19. data/lib/bio-vcf/vcfrecord.rb +30 -15
  20. data/ragel/gen_vcfheaderline_parser.rl +68 -25
  21. data/ragel/generate.sh +4 -1
  22. data/template/vcf2json.erb +16 -16
  23. data/template/vcf2json_full_header.erb +16 -17
  24. data/template/vcf2json_use_meta.erb +35 -35
  25. data/test/data/input/gatk_exome.vcf +237 -0
  26. data/test/data/input/gatk_wgs.vcf +1000 -0
  27. data/test/data/input/test.bed +632 -0
  28. data/test/data/regression/eval_once-stderr.new +1 -0
  29. data/test/data/regression/eval_once.new +1 -0
  30. data/test/data/regression/eval_once.ref +1 -0
  31. data/test/data/regression/eval_r.info.dp-stderr.new +4 -0
  32. data/test/data/regression/eval_r.info.dp.new +150 -0
  33. data/test/data/regression/ifilter_s.dp-stderr.new +28 -0
  34. data/test/data/regression/ifilter_s.dp.new +31 -0
  35. data/test/data/regression/r.info.dp-stderr.new +4 -0
  36. data/test/data/regression/r.info.dp.new +147 -0
  37. data/test/data/regression/rewrite.info.sample-stderr.new +4 -0
  38. data/test/data/regression/rewrite.info.sample.new +150 -0
  39. data/test/data/regression/s.dp-stderr.new +12 -0
  40. data/test/data/regression/s.dp.new +145 -0
  41. data/test/data/regression/seval_s.dp-stderr.new +4 -0
  42. data/test/data/regression/seval_s.dp.new +36 -0
  43. data/test/data/regression/sfilter_seval_s.dp-stderr.new +12 -0
  44. data/test/data/regression/sfilter_seval_s.dp.new +31 -0
  45. data/test/data/regression/thread4-stderr.new +4 -0
  46. data/test/data/regression/thread4.new +150 -0
  47. data/test/data/regression/thread4_4-stderr.new +15 -0
  48. data/test/data/regression/thread4_4.new +150 -0
  49. data/test/data/regression/thread4_4_failed_filter-stderr.new +5 -0
  50. data/test/data/regression/thread4_4_failed_filter-stderr.ref +5 -2
  51. data/test/data/regression/thread4_4_failed_filter.new +110 -0
  52. data/test/data/regression/vcf2json_full_header-stderr.new +4 -0
  53. data/test/data/regression/vcf2json_full_header.new +225 -0
  54. data/test/data/regression/vcf2json_full_header.ref +222 -258
  55. data/test/data/regression/vcf2json_use_meta-stderr.new +4 -0
  56. data/test/data/regression/vcf2json_use_meta.new +4697 -0
  57. data/test/data/regression/vcf2json_use_meta.ref +4697 -0
  58. data/test/performance/metrics.md +18 -1
  59. data/test/tmp/test.vcf +12469 -0
  60. metadata +38 -62
  61. data/Gemfile.lock +0 -81
  62. data/ragel/gen_vcfheaderline_parser.rb +0 -483
data/test/data/regression/eval_once-stderr.new ADDED
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+ bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
data/test/data/regression/eval_once.new ADDED
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+ {"UnifiedGenotyper"=>{"ID"=>"UnifiedGenotyper", "Version"=>"2.8-1-g932cd3a", "Date"=>"Sat Jan 25 10:33:56 CET 2014", "Epoch"=>1390642436187, "CommandLineOptions"=>"analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.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 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 num_threads=1 num_cpu_threads_per_data_thread=1 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=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"}}
data/test/data/regression/eval_once.ref ADDED
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+ {"UnifiedGenotyper"=>{"ID"=>"UnifiedGenotyper", "Version"=>"2.8-1-g932cd3a", "Date"=>"Sat Jan 25 10:33:56 CET 2014", "Epoch"=>1390642436187, "CommandLineOptions"=>"analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.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 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 num_threads=1 num_cpu_threads_per_data_thread=1 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=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"}}
data/test/data/regression/eval_r.info.dp-stderr.new ADDED
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+ bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
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+ Waiting up to 180 seconds for pid=3644 to complete
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+ OK pid=3644, processing /tmp/bio-vcf_20150816-3642-1j5rn5y/000001-bio-vcf
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+ Processing /tmp/bio-vcf_20150816-3642-1j5rn5y/000001-bio-vcf
data/test/data/regression/eval_r.info.dp.new ADDED
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+ ##fileformat=VCFv4.1
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+ ##FILTER=<ID=LowQual,Description="Low quality">
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+ ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
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+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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+ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
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+ ##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.8-1-g932cd3a,Date="Sat Jan 25 10:33:56 CET 2014",Epoch=1390642436187,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.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 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 num_threads=1 num_cpu_threads_per_data_thread=1 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=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
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+ ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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+ ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
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+ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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+ ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
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+ ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
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+ ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
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+ ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
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+ ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
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+ ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
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+ ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
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+ ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
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+ ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
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+ ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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+ ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
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+ ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
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+ ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
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+ ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
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+ ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
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+ ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
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+ ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
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+ ##contig=<ID=1,length=249250621,assembly=b37>
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+ ##contig=<ID=2,length=243199373,assembly=b37>
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+ ##contig=<ID=3,length=198022430,assembly=b37>
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+ ##contig=<ID=4,length=191154276,assembly=b37>
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+ ##contig=<ID=5,length=180915260,assembly=b37>
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+ ##contig=<ID=6,length=171115067,assembly=b37>
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+ ##contig=<ID=7,length=159138663,assembly=b37>
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+ ##contig=<ID=8,length=146364022,assembly=b37>
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+ ##contig=<ID=9,length=141213431,assembly=b37>
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+ ##contig=<ID=10,length=135534747,assembly=b37>
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+ ##contig=<ID=11,length=135006516,assembly=b37>
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+ ##contig=<ID=12,length=133851895,assembly=b37>
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+ ##contig=<ID=13,length=115169878,assembly=b37>
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+ ##contig=<ID=14,length=107349540,assembly=b37>
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+ ##contig=<ID=15,length=102531392,assembly=b37>
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+ ##contig=<ID=16,length=90354753,assembly=b37>
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+ ##contig=<ID=17,length=81195210,assembly=b37>
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+ ##contig=<ID=18,length=78077248,assembly=b37>
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+ ##contig=<ID=19,length=59128983,assembly=b37>
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+ ##contig=<ID=20,length=63025520,assembly=b37>
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+ ##contig=<ID=21,length=48129895,assembly=b37>
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+ ##contig=<ID=22,length=51304566,assembly=b37>
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+ ##contig=<ID=X,length=155270560,assembly=b37>
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+ ##contig=<ID=Y,length=59373566,assembly=b37>
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+ ##contig=<ID=MT,length=16569,assembly=b37>
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+ ##contig=<ID=GL000207.1,length=4262,assembly=b37>
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+ ##contig=<ID=GL000226.1,length=15008,assembly=b37>
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+ ##contig=<ID=GL000229.1,length=19913,assembly=b37>
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+ ##contig=<ID=GL000231.1,length=27386,assembly=b37>
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+ ##contig=<ID=GL000210.1,length=27682,assembly=b37>
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+ ##contig=<ID=GL000239.1,length=33824,assembly=b37>
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+ ##contig=<ID=GL000235.1,length=34474,assembly=b37>
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+ ##contig=<ID=GL000201.1,length=36148,assembly=b37>
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+ ##contig=<ID=GL000247.1,length=36422,assembly=b37>
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+ ##contig=<ID=GL000245.1,length=36651,assembly=b37>
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+ ##contig=<ID=GL000197.1,length=37175,assembly=b37>
65
+ ##contig=<ID=GL000203.1,length=37498,assembly=b37>
66
+ ##contig=<ID=GL000246.1,length=38154,assembly=b37>
67
+ ##contig=<ID=GL000249.1,length=38502,assembly=b37>
68
+ ##contig=<ID=GL000196.1,length=38914,assembly=b37>
69
+ ##contig=<ID=GL000248.1,length=39786,assembly=b37>
70
+ ##contig=<ID=GL000244.1,length=39929,assembly=b37>
71
+ ##contig=<ID=GL000238.1,length=39939,assembly=b37>
72
+ ##contig=<ID=GL000202.1,length=40103,assembly=b37>
73
+ ##contig=<ID=GL000234.1,length=40531,assembly=b37>
74
+ ##contig=<ID=GL000232.1,length=40652,assembly=b37>
75
+ ##contig=<ID=GL000206.1,length=41001,assembly=b37>
76
+ ##contig=<ID=GL000240.1,length=41933,assembly=b37>
77
+ ##contig=<ID=GL000236.1,length=41934,assembly=b37>
78
+ ##contig=<ID=GL000241.1,length=42152,assembly=b37>
79
+ ##contig=<ID=GL000243.1,length=43341,assembly=b37>
80
+ ##contig=<ID=GL000242.1,length=43523,assembly=b37>
81
+ ##contig=<ID=GL000230.1,length=43691,assembly=b37>
82
+ ##contig=<ID=GL000237.1,length=45867,assembly=b37>
83
+ ##contig=<ID=GL000233.1,length=45941,assembly=b37>
84
+ ##contig=<ID=GL000204.1,length=81310,assembly=b37>
85
+ ##contig=<ID=GL000198.1,length=90085,assembly=b37>
86
+ ##contig=<ID=GL000208.1,length=92689,assembly=b37>
87
+ ##contig=<ID=GL000191.1,length=106433,assembly=b37>
88
+ ##contig=<ID=GL000227.1,length=128374,assembly=b37>
89
+ ##contig=<ID=GL000228.1,length=129120,assembly=b37>
90
+ ##contig=<ID=GL000214.1,length=137718,assembly=b37>
91
+ ##contig=<ID=GL000221.1,length=155397,assembly=b37>
92
+ ##contig=<ID=GL000209.1,length=159169,assembly=b37>
93
+ ##contig=<ID=GL000218.1,length=161147,assembly=b37>
94
+ ##contig=<ID=GL000220.1,length=161802,assembly=b37>
95
+ ##contig=<ID=GL000213.1,length=164239,assembly=b37>
96
+ ##contig=<ID=GL000211.1,length=166566,assembly=b37>
97
+ ##contig=<ID=GL000199.1,length=169874,assembly=b37>
98
+ ##contig=<ID=GL000217.1,length=172149,assembly=b37>
99
+ ##contig=<ID=GL000216.1,length=172294,assembly=b37>
100
+ ##contig=<ID=GL000215.1,length=172545,assembly=b37>
101
+ ##contig=<ID=GL000205.1,length=174588,assembly=b37>
102
+ ##contig=<ID=GL000219.1,length=179198,assembly=b37>
103
+ ##contig=<ID=GL000224.1,length=179693,assembly=b37>
104
+ ##contig=<ID=GL000223.1,length=180455,assembly=b37>
105
+ ##contig=<ID=GL000195.1,length=182896,assembly=b37>
106
+ ##contig=<ID=GL000212.1,length=186858,assembly=b37>
107
+ ##contig=<ID=GL000222.1,length=186861,assembly=b37>
108
+ ##contig=<ID=GL000200.1,length=187035,assembly=b37>
109
+ ##contig=<ID=GL000193.1,length=189789,assembly=b37>
110
+ ##contig=<ID=GL000194.1,length=191469,assembly=b37>
111
+ ##contig=<ID=GL000225.1,length=211173,assembly=b37>
112
+ ##contig=<ID=GL000192.1,length=547496,assembly=b37>
113
+ ##reference=file:human_g1k_v37.fasta
114
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2
115
+ 1518
116
+ 1433
117
+ 1440
118
+ 1460
119
+ 1500
120
+ 1537
121
+ 1641
122
+ 129
123
+ 28
124
+ 22
125
+ 18
126
+ 939
127
+ 721
128
+ 703
129
+ 929
130
+ 692
131
+ 1149
132
+ 1108
133
+ 830
134
+ 764
135
+ 809
136
+ 754
137
+ 719
138
+ 1083
139
+ 1092
140
+ 1089
141
+ 1050
142
+ 939
143
+ 1004
144
+ 1090
145
+ 992
146
+ 636
147
+ 1213
148
+ 904
149
+ 398
150
+ 526
data/test/data/regression/ifilter_s.dp-stderr.new ADDED
@@ -0,0 +1,28 @@
1
+ bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
+ Waiting up to 180 seconds for pid=3632 to complete
3
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
4
+ [:filter, "s.dp>100"]
5
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
6
+ [:filter, "s.dp>100"]
7
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
8
+ [:filter, "s.dp>100"]
9
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
10
+ [:filter, "s.dp>100"]
11
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
12
+ [:filter, "s.dp>100"]
13
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
14
+ [:filter, "s.dp>100"]
15
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
16
+ [:filter, "s.dp>100"]
17
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
18
+ [:filter, "s.dp>100"]
19
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
20
+ [:filter, "s.dp>100"]
21
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
22
+ [:filter, "s.dp>100"]
23
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
24
+ [:filter, "s.dp>100"]
25
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
26
+ [:filter, "s.dp>100"]
27
+ OK pid=3632, processing /tmp/bio-vcf_20150816-3629-1g0u53a/000001-bio-vcf
28
+ Processing /tmp/bio-vcf_20150816-3629-1g0u53a/000001-bio-vcf
data/test/data/regression/ifilter_s.dp.new ADDED
@@ -0,0 +1,31 @@
1
+ 1 10257 159 242 249 249 186 212 218
2
+ 1 10291 165 249 249 247 161 163 189
3
+ 1 10297 182 246 250 246 165 158 183
4
+ 1 10303 198 247 248 248 172 157 182
5
+ 1 10315 212 246 242 245 190 157 189
6
+ 1 10321 218 246 248 248 193 164 196
7
+ 1 10327 237 238 229 237 209 183 210
8
+ 1 12783 58 164 144 182 126 103 158
9
+ 1 13116 32 131 102 152 104 88 109
10
+ 1 13118 34 129 101 145 99 85 108
11
+ 1 13178 52 172 137 172 129 119 148
12
+ 1 13302 36 136 99 146 90 65 117
13
+ 1 13757 53 201 181 250 152 130 182
14
+ 1 13868 75 192 182 224 142 111 167
15
+ 1 13896 62 135 143 175 112 81 121
16
+ 1 14354 43 158 115 145 72 119
17
+ 1 14464 51 155 141 150 83 89 140
18
+ 1 14673 36 142 117 157 95 76 131
19
+ 1 14699 43 128 109 147 98 78 114
20
+ 1 14907 57 216 162 205 153 118 158
21
+ 1 14930 68 216 170 210 136 125 164
22
+ 1 14933 68 216 169 212 132 128 164
23
+ 1 14948 63 192 181 211 129 121 153
24
+ 1 14976 56 166 161 196 109 116 135
25
+ 1 15118 46 198 129 230 113 126 158
26
+ 1 15190 53 208 170 200 126 145 179
27
+ 1 15211 54 183 161 171 120 134 168
28
+ 1 15274 37 121 102 137 71 67 98
29
+ 1 15447 46 242 183 226 137 173 175
30
+ 1 15688 37 182 147 184 100 101 148
31
+ 1 16103 50 79 86 106 60 61 84
data/test/data/regression/r.info.dp-stderr.new ADDED
@@ -0,0 +1,4 @@
1
+ bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
+ Waiting up to 180 seconds for pid=3546 to complete
3
+ OK pid=3546, processing /tmp/bio-vcf_20150816-3543-hoqahc/000001-bio-vcf
4
+ Processing /tmp/bio-vcf_20150816-3543-hoqahc/000001-bio-vcf
data/test/data/regression/r.info.dp.new ADDED
@@ -0,0 +1,147 @@
1
+ ##fileformat=VCFv4.1
2
+ ##FILTER=<ID=LowQual,Description="Low quality">
3
+ ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
4
+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
5
+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
6
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
7
+ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
8
+ ##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.8-1-g932cd3a,Date="Sat Jan 25 10:33:56 CET 2014",Epoch=1390642436187,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.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 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 num_threads=1 num_cpu_threads_per_data_thread=1 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=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
9
+ ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
10
+ ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
11
+ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
12
+ ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
13
+ ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
14
+ ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
15
+ ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
16
+ ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
17
+ ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
18
+ ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
19
+ ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
20
+ ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
21
+ ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
22
+ ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
23
+ ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
24
+ ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
25
+ ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
26
+ ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
27
+ ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
28
+ ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
29
+ ##contig=<ID=1,length=249250621,assembly=b37>
30
+ ##contig=<ID=2,length=243199373,assembly=b37>
31
+ ##contig=<ID=3,length=198022430,assembly=b37>
32
+ ##contig=<ID=4,length=191154276,assembly=b37>
33
+ ##contig=<ID=5,length=180915260,assembly=b37>
34
+ ##contig=<ID=6,length=171115067,assembly=b37>
35
+ ##contig=<ID=7,length=159138663,assembly=b37>
36
+ ##contig=<ID=8,length=146364022,assembly=b37>
37
+ ##contig=<ID=9,length=141213431,assembly=b37>
38
+ ##contig=<ID=10,length=135534747,assembly=b37>
39
+ ##contig=<ID=11,length=135006516,assembly=b37>
40
+ ##contig=<ID=12,length=133851895,assembly=b37>
41
+ ##contig=<ID=13,length=115169878,assembly=b37>
42
+ ##contig=<ID=14,length=107349540,assembly=b37>
43
+ ##contig=<ID=15,length=102531392,assembly=b37>
44
+ ##contig=<ID=16,length=90354753,assembly=b37>
45
+ ##contig=<ID=17,length=81195210,assembly=b37>
46
+ ##contig=<ID=18,length=78077248,assembly=b37>
47
+ ##contig=<ID=19,length=59128983,assembly=b37>
48
+ ##contig=<ID=20,length=63025520,assembly=b37>
49
+ ##contig=<ID=21,length=48129895,assembly=b37>
50
+ ##contig=<ID=22,length=51304566,assembly=b37>
51
+ ##contig=<ID=X,length=155270560,assembly=b37>
52
+ ##contig=<ID=Y,length=59373566,assembly=b37>
53
+ ##contig=<ID=MT,length=16569,assembly=b37>
54
+ ##contig=<ID=GL000207.1,length=4262,assembly=b37>
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+ ##contig=<ID=GL000226.1,length=15008,assembly=b37>
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+ ##contig=<ID=GL000229.1,length=19913,assembly=b37>
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+ ##contig=<ID=GL000231.1,length=27386,assembly=b37>
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+ ##contig=<ID=GL000210.1,length=27682,assembly=b37>
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+ ##contig=<ID=GL000239.1,length=33824,assembly=b37>
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+ ##contig=<ID=GL000235.1,length=34474,assembly=b37>
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+ ##contig=<ID=GL000201.1,length=36148,assembly=b37>
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+ ##contig=<ID=GL000247.1,length=36422,assembly=b37>
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+ ##contig=<ID=GL000245.1,length=36651,assembly=b37>
64
+ ##contig=<ID=GL000197.1,length=37175,assembly=b37>
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+ ##contig=<ID=GL000203.1,length=37498,assembly=b37>
66
+ ##contig=<ID=GL000246.1,length=38154,assembly=b37>
67
+ ##contig=<ID=GL000249.1,length=38502,assembly=b37>
68
+ ##contig=<ID=GL000196.1,length=38914,assembly=b37>
69
+ ##contig=<ID=GL000248.1,length=39786,assembly=b37>
70
+ ##contig=<ID=GL000244.1,length=39929,assembly=b37>
71
+ ##contig=<ID=GL000238.1,length=39939,assembly=b37>
72
+ ##contig=<ID=GL000202.1,length=40103,assembly=b37>
73
+ ##contig=<ID=GL000234.1,length=40531,assembly=b37>
74
+ ##contig=<ID=GL000232.1,length=40652,assembly=b37>
75
+ ##contig=<ID=GL000206.1,length=41001,assembly=b37>
76
+ ##contig=<ID=GL000240.1,length=41933,assembly=b37>
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+ ##contig=<ID=GL000236.1,length=41934,assembly=b37>
78
+ ##contig=<ID=GL000241.1,length=42152,assembly=b37>
79
+ ##contig=<ID=GL000243.1,length=43341,assembly=b37>
80
+ ##contig=<ID=GL000242.1,length=43523,assembly=b37>
81
+ ##contig=<ID=GL000230.1,length=43691,assembly=b37>
82
+ ##contig=<ID=GL000237.1,length=45867,assembly=b37>
83
+ ##contig=<ID=GL000233.1,length=45941,assembly=b37>
84
+ ##contig=<ID=GL000204.1,length=81310,assembly=b37>
85
+ ##contig=<ID=GL000198.1,length=90085,assembly=b37>
86
+ ##contig=<ID=GL000208.1,length=92689,assembly=b37>
87
+ ##contig=<ID=GL000191.1,length=106433,assembly=b37>
88
+ ##contig=<ID=GL000227.1,length=128374,assembly=b37>
89
+ ##contig=<ID=GL000228.1,length=129120,assembly=b37>
90
+ ##contig=<ID=GL000214.1,length=137718,assembly=b37>
91
+ ##contig=<ID=GL000221.1,length=155397,assembly=b37>
92
+ ##contig=<ID=GL000209.1,length=159169,assembly=b37>
93
+ ##contig=<ID=GL000218.1,length=161147,assembly=b37>
94
+ ##contig=<ID=GL000220.1,length=161802,assembly=b37>
95
+ ##contig=<ID=GL000213.1,length=164239,assembly=b37>
96
+ ##contig=<ID=GL000211.1,length=166566,assembly=b37>
97
+ ##contig=<ID=GL000199.1,length=169874,assembly=b37>
98
+ ##contig=<ID=GL000217.1,length=172149,assembly=b37>
99
+ ##contig=<ID=GL000216.1,length=172294,assembly=b37>
100
+ ##contig=<ID=GL000215.1,length=172545,assembly=b37>
101
+ ##contig=<ID=GL000205.1,length=174588,assembly=b37>
102
+ ##contig=<ID=GL000219.1,length=179198,assembly=b37>
103
+ ##contig=<ID=GL000224.1,length=179693,assembly=b37>
104
+ ##contig=<ID=GL000223.1,length=180455,assembly=b37>
105
+ ##contig=<ID=GL000195.1,length=182896,assembly=b37>
106
+ ##contig=<ID=GL000212.1,length=186858,assembly=b37>
107
+ ##contig=<ID=GL000222.1,length=186861,assembly=b37>
108
+ ##contig=<ID=GL000200.1,length=187035,assembly=b37>
109
+ ##contig=<ID=GL000193.1,length=189789,assembly=b37>
110
+ ##contig=<ID=GL000194.1,length=191469,assembly=b37>
111
+ ##contig=<ID=GL000225.1,length=211173,assembly=b37>
112
+ ##contig=<ID=GL000192.1,length=547496,assembly=b37>
113
+ ##reference=file:human_g1k_v37.fasta
114
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2
115
+ 1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551 GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972
116
+ 1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640 GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372
117
+ 1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927 GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485
118
+ 1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756 GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413
119
+ 1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373 GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450
120
+ 1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815 GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522
121
+ 1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957 GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550
122
+ 1 10583 . G A 699.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-4.714;DP=129;Dels=0.00;FS=7.556;HaplotypeScore=0.6677;MLEAC=7;MLEAF=0.500;MQ=41.33;MQ0=2;MQRankSum=-2.309;QD=5.43;ReadPosRankSum=-0.296 GT:AD:DP:GQ:PL 0/1:5,3:8:58:58,0,133 0/1:12,12:24:99:231,0,287 0/1:16,4:21:38:38,0,491 0/1:19,4:23:57:57,0,494 0/1:9,6:15:99:140,0,180 0/1:11,8:19:99:173,0,235 0/1:15,4:19:42:42,0,344
123
+ 1 12783 . G A 4330.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=12.671;DP=939;Dels=0.00;FS=0.000;HaplotypeScore=1.4998;MLEAC=7;MLEAF=0.500;MQ=14.64;MQ0=602;MQRankSum=-3.992;QD=4.61;ReadPosRankSum=0.195 GT:AD:DP:GQ:PL 0/1:24,34:58:82:174,0,82 0/1:80,84:164:99:658,0,433 0/1:59,85:144:99:670,0,407 0/1:68,114:182:99:1074,0,463 0/1:58,68:126:99:437,0,310 0/1:37,66:103:99:446,0,369 0/1:62,96:158:99:911,0,417
124
+ 1 13116 . T G 2592.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.563;DP=721;Dels=0.00;FS=381.256;HaplotypeScore=2.5606;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=222;MQRankSum=-14.896;QD=3.60;ReadPosRankSum=3.079 GT:AD:DP:GQ:PL 0/1:20,12:32:92:92,0,300 0/1:84,47:131:99:479,0,1548 0/1:65,37:102:99:441,0,1153 0/1:94,57:152:99:584,0,1993 0/1:61,43:104:99:360,0,1199 0/1:54,33:88:99:221,0,986 0/1:62,47:109:99:455,0,1128
125
+ 1 13118 . A G 2317.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-9.647;DP=703;Dels=0.00;FS=362.380;HaplotypeScore=2.3393;MLEAC=7;MLEAF=0.500;MQ=23.54;MQ0=228;MQRankSum=-14.592;QD=3.30;ReadPosRankSum=3.437 GT:AD:DP:GQ:PL 0/1:21,13:34:95:95,0,277 0/1:82,47:129:99:444,0,1445 0/1:65,36:101:99:412,0,1179 0/1:92,53:145:99:455,0,1989 0/1:58,40:99:99:312,0,1216 0/1:52,33:85:99:186,0,1000 0/1:61,47:108:99:453,0,1079
126
+ 1 13178 . G A 72.69 . AC=2;AF=0.143;AN=14;BaseQRankSum=-2.194;DP=929;Dels=0.00;FS=8.154;HaplotypeScore=1.8585;MLEAC=2;MLEAF=0.143;MQ=13.49;MQ0=590;MQRankSum=-3.030;QD=0.38;ReadPosRankSum=-0.383 GT:AD:DP:GQ:PL 0/1:49,3:52:11:11,0,292 0/0:161,11:172:60:0,60,1328 0/1:122,15:137:99:99,0,936 0/0:164,8:172:99:0,112,1436 0/0:120,9:129:62:0,62,771 0/0:113,6:119:12:0,12,885 0/0:138,10:148:99:0,112,1596
127
+ 1 13302 . C T 1067.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=11.584;DP=692;Dels=0.00;FS=86.736;HaplotypeScore=2.8260;MLEAC=6;MLEAF=0.429;MQ=27.08;MQ0=150;MQRankSum=-14.794;QD=1.63;ReadPosRankSum=-9.193 GT:AD:DP:GQ:PL 0/0:26,10:36:41:0,41,616 0/1:91,45:136:99:183,0,2085 0/1:71,28:99:86:86,0,1557 0/1:96,50:146:99:333,0,2098 0/1:55,34:90:99:283,0,1321 0/1:47,18:65:99:157,0,943 0/1:89,28:117:67:67,0,1921
128
+ 1 13757 . G A 271.89 . AC=2;AF=0.143;AN=14;BaseQRankSum=2.916;DP=1149;Dels=0.00;FS=11.172;HaplotypeScore=7.1466;MLEAC=2;MLEAF=0.143;MQ=18.17;MQ0=374;MQRankSum=3.990;QD=0.87;ReadPosRankSum=1.309 GT:AD:DP:GQ:PL 0/0:47,4:53:16:0,16,344 0/0:185,16:201:60:0,60,2690 0/1:157,24:181:99:162,0,2556 0/0:232,18:250:99:0,137,3600 0/0:139,13:152:15:0,15,2266 0/1:114,16:130:99:147,0,1525 0/0:168,14:182:2:0,2,2230
129
+ 1 13868 . A G 1481.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=2.036;DP=1108;Dels=0.00;FS=4.601;HaplotypeScore=6.7136;MLEAC=7;MLEAF=0.500;MQ=13.23;MQ0=622;MQRankSum=1.659;QD=1.34;ReadPosRankSum=0.283 GT:AD:DP:GQ:PL 0/1:60,15:75:80:80,0,568 0/1:146,46:192:99:289,0,1030 0/1:146,36:182:99:203,0,1001 0/1:172,52:224:99:222,0,1150 0/1:106,36:142:99:181,0,621 0/1:79,32:111:99:126,0,467 0/1:129,38:167:99:420,0,767
130
+ 1 13896 . C A 389.42 . AC=6;AF=0.429;AN=14;BaseQRankSum=-0.743;DP=830;Dels=0.00;FS=0.000;HaplotypeScore=1.6931;MLEAC=6;MLEAF=0.429;MQ=11.88;MQ0=518;MQRankSum=-1.292;QD=0.54;ReadPosRankSum=0.433 GT:AD:DP:GQ:PL 0/1:50,12:62:99:107,0,367 0/1:107,28:135:40:40,0,660 0/1:120,23:143:37:37,0,675 0/1:144,31:175:99:172,0,690 0/0:98,14:112:42:0,42,577 0/1:65,16:81:34:34,0,290 0/1:102,19:121:41:41,0,677
131
+ 1 14354 . C A 109.72 . AC=3;AF=0.250;AN=12;BaseQRankSum=-2.527;DP=764;Dels=0.00;FS=0.000;HaplotypeScore=0.3231;MLEAC=3;MLEAF=0.250;MQ=5.02;MQ0=710;MQRankSum=1.079;QD=0.47;ReadPosRankSum=-0.178 GT:AD:DP:GQ:PL 0/1:36,7:43:68:68,0,75 0/0:141,17:158:9:0,9,86 0/1:103,12:115:42:42,0,72 0/0:132,13:145:21:0,21,201 ./. 0/1:62,10:72:38:38,0,117 0/0:108,11:119:9:0,9,86
132
+ 1 14464 . A T 3945.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=0.104;DP=809;Dels=0.00;FS=38.588;HaplotypeScore=5.8354;MLEAC=7;MLEAF=0.500;MQ=23.21;MQ0=241;MQRankSum=6.859;QD=4.88;ReadPosRankSum=-0.294 GT:AD:DP:GQ:PL 0/1:41,10:51:99:183,0,569 0/1:107,48:155:99:829,0,1388 0/1:99,42:141:99:691,0,1103 0/1:114,36:150:99:454,0,1544 0/1:48,35:83:99:781,0,561 0/1:64,25:89:99:409,0,781 0/1:102,38:140:99:638,0,1310
133
+ 1 14673 . G C 1012.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.674;DP=754;Dels=0.00;FS=115.496;HaplotypeScore=14.9167;MLEAC=7;MLEAF=0.500;MQ=23.97;MQ0=268;MQRankSum=-1.459;QD=1.34;ReadPosRankSum=-3.039 GT:AD:DP:GQ:PL 0/1:28,8:36:34:34,0,409 0/1:117,25:142:99:125,0,1964 0/1:87,30:117:99:214,0,1506 0/1:130,27:157:99:193,0,2076 0/1:77,18:95:99:114,0,1273 0/1:49,27:76:99:200,0,719 0/1:103,28:131:99:172,0,1620
134
+ 1 14699 . C G 64.65 . AC=2;AF=0.143;AN=14;BaseQRankSum=6.064;DP=719;Dels=0.00;FS=29.480;HaplotypeScore=5.5900;MLEAC=2;MLEAF=0.143;MQ=24.79;MQ0=233;MQRankSum=-8.066;QD=0.27;ReadPosRankSum=-0.696 GT:AD:DP:GQ:PL 0/0:35,6:43:51:0,51,720 0/1:91,37:128:59:59,0,1859 0/0:80,29:109:99:0,101,1700 0/0:113,34:147:14:0,14,1987 0/0:72,26:98:37:0,37,1319 0/0:53,25:78:78:0,78,1035 0/1:84,30:114:44:44,0,1326
135
+ 1 14907 . A G 9688.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.299;DP=1083;Dels=0.00;FS=20.983;HaplotypeScore=11.4413;MLEAC=7;MLEAF=0.500;MQ=33.27;MQ0=51;MQRankSum=1.076;QD=8.95;ReadPosRankSum=0.653 GT:AD:DP:GQ:PL 0/1:27,30:57:99:603,0,550 0/1:117,99:216:99:2024,0,2888 0/1:91,71:162:99:1489,0,1990 0/1:119,86:205:99:1876,0,2588 0/1:100,53:153:99:1001,0,2297 0/1:59,59:118:99:1240,0,1241 0/1:91,67:158:99:1495,0,2003
136
+ 1 14930 . A G 8665.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-13.760;DP=1092;Dels=0.00;FS=17.240;HaplotypeScore=20.0469;MLEAC=7;MLEAF=0.500;MQ=34.72;MQ0=22;MQRankSum=1.127;QD=7.94;ReadPosRankSum=0.785 GT:AD:DP:GQ:PL 0/1:32,36:68:99:609,0,659 0/1:123,92:216:99:1636,0,3225 0/1:92,78:170:99:1449,0,2202 0/1:123,86:210:99:1748,0,3028 0/1:85,50:136:99:802,0,2117 0/1:62,63:125:99:1072,0,1437 0/1:92,71:164:99:1389,0,2055
137
+ 1 14933 . G A 248.54 . AC=3;AF=0.214;AN=14;BaseQRankSum=1.588;DP=1089;Dels=0.00;FS=14.333;HaplotypeScore=19.7793;MLEAC=3;MLEAF=0.214;MQ=34.91;MQ0=18;MQRankSum=1.439;QD=0.45;ReadPosRankSum=0.752 GT:AD:DP:GQ:PL 0/0:59,9:68:1:0,1,1361 0/1:192,24:216:99:125,0,4941 0/0:160,9:169:99:0,142,4118 0/1:191,21:212:39:39,0,4848 0/0:126,6:132:99:0,210,3367 0/1:113,15:128:99:124,0,2578 0/0:154,10:164:99:0,158,3934
138
+ 1 14948 . G A 570.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=9.167;DP=1050;Dels=0.00;FS=11.131;HaplotypeScore=6.4398;MLEAC=7;MLEAF=0.500;MQ=32.69;MQ0=53;MQRankSum=0.017;QD=0.54;ReadPosRankSum=-1.181 GT:AD:DP:GQ:PL 0/1:56,7:63:79:79,0,1134 0/1:168,24:192:70:70,0,3900 0/1:160,21:181:99:147,0,3515 0/1:188,23:211:57:57,0,4113 0/1:115,14:129:32:32,0,2406 0/1:103,18:121:99:173,0,2016 0/1:132,21:153:52:52,0,2861
139
+ 1 14976 . G A 195.07 . AC=3;AF=0.214;AN=14;BaseQRankSum=7.340;DP=939;Dels=0.00;FS=32.492;HaplotypeScore=4.6786;MLEAC=3;MLEAF=0.214;MQ=27.87;MQ0=167;MQRankSum=1.477;QD=0.53;ReadPosRankSum=-0.560 GT:AD:DP:GQ:PL 0/1:50,6:56:12:12,0,929 0/0:152,14:166:81:0,81,3159 0/0:152,9:161:99:0,113,2885 0/1:174,22:196:99:127,0,3211 0/0:100,9:109:97:0,97,1900 0/1:103,13:116:97:97,0,1548 0/0:122,13:135:55:0,55,2246
140
+ 1 15118 . A G 2503.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-5.645;DP=1004;Dels=0.00;FS=0.313;HaplotypeScore=4.1078;MLEAC=7;MLEAF=0.500;MQ=21.49;MQ0=207;MQRankSum=-0.007;QD=2.49;ReadPosRankSum=-0.291 GT:AD:DP:GQ:PL 0/1:38,8:46:50:50,0,575 0/1:148,50:198:99:671,0,2598 0/1:97,32:129:99:358,0,1911 0/1:176,53:230:99:700,0,2989 0/1:91,19:113:99:146,0,1741 0/1:92,31:126:99:347,0,1543 0/1:126,30:158:99:271,0,2193
141
+ 1 15190 . G A 2564.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=11.094;DP=1090;Dels=0.00;FS=0.297;HaplotypeScore=4.3151;MLEAC=7;MLEAF=0.500;MQ=26.11;MQ0=187;MQRankSum=-0.724;QD=2.35;ReadPosRankSum=0.530 GT:AD:DP:GQ:PL 0/1:42,11:53:99:177,0,696 0/1:157,51:208:99:839,0,3145 0/1:142,28:170:91:91,0,2919 0/1:160,40:200:99:499,0,2815 0/1:109,17:126:99:167,0,2363 0/1:111,34:145:99:554,0,2268 0/1:141,38:179:99:277,0,2827
142
+ 1 15211 . T G 14032.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-11.292;DP=992;Dels=0.00;FS=0.281;HaplotypeScore=11.0809;MLEAC=7;MLEAF=0.500;MQ=27.20;MQ0=159;MQRankSum=3.859;QD=14.15;ReadPosRankSum=-1.972 GT:AD:DP:GQ:PL 0/1:19,35:54:99:858,0,183 0/1:63,120:183:99:2771,0,960 0/1:50,111:161:99:2213,0,740 0/1:58,113:171:99:2326,0,685 0/1:39,81:120:99:1707,0,678 0/1:38,96:134:99:2126,0,499 0/1:61,107:168:99:2071,0,895
143
+ 1 15274 . A G,T 8909.81 . AC=7,7;AF=0.500,0.500;AN=14;BaseQRankSum=2.416;DP=636;Dels=0.00;FS=0.000;HaplotypeScore=5.1061;MLEAC=7,7;MLEAF=0.500,0.500;MQ=22.77;MQ0=195;MQRankSum=2.299;QD=14.01;ReadPosRankSum=1.707 GT:AD:DP:GQ:PL 1/2:1,14,22:37:99:717,494,467,224,0,170 1/2:1,45,75:121:99:1922,1334,1265,588,0,441 1/2:0,31,71:102:99:1960,1563,1515,396,0,222 1/2:1,59,77:137:99:2009,1376,1298,633,0,486 1/2:0,18,52:71:62:938,789,771,149,0,62 1/2:0,29,38:67:99:1141,883,853,258,0,162 1/2:0,38,60:98:99:1464,1064,1016,399,0,285
144
+ 1 15447 . A G 109.56 . AC=3;AF=0.214;AN=14;BaseQRankSum=-9.704;DP=1213;Dels=0.00;FS=0.000;HaplotypeScore=16.4636;MLEAC=3;MLEAF=0.214;MQ=19.12;MQ0=346;MQRankSum=-0.997;QD=0.20;ReadPosRankSum=-1.088 GT:AD:DP:GQ:PL 0/0:42,4:46:34:0,34,690 0/0:220,22:242:99:0,99,3639 0/0:167,16:183:42:0,42,2582 0/1:201,25:226:78:78,0,2854 0/1:121,16:137:39:39,0,1877 0/0:160,13:173:99:0,139,2724 0/1:157,18:175:34:34,0,2472
145
+ 1 15688 . C T 54.29 . AC=2;AF=0.143;AN=14;BaseQRankSum=-8.686;DP=904;Dels=0.00;FS=11.971;HaplotypeScore=3.1454;MLEAC=2;MLEAF=0.143;MQ=16.75;MQ0=361;MQRankSum=-0.069;QD=0.16;ReadPosRankSum=0.355 GT:AD:DP:GQ:PL 0/0:34,3:37:15:0,15,335 0/0:166,16:182:61:0,61,2190 0/1:131,16:147:69:69,0,1563 0/1:167,17:184:22:22,0,1894 0/0:88,12:100:15:0,15,1099 0/0:88,13:101:1:0,1,1126 0/0:132,16:148:18:0,18,1706
146
+ 1 16068 . T C 377.22 . AC=4;AF=0.286;AN=14;BaseQRankSum=-7.618;DP=398;Dels=0.00;FS=12.349;HaplotypeScore=1.8069;MLEAC=4;MLEAF=0.286;MQ=26.64;MQ0=64;MQRankSum=-4.589;QD=1.80;ReadPosRankSum=-0.448 GT:AD:DP:GQ:PL 0/1:18,15:33:99:182,0,404 0/0:51,6:57:31:0,31,815 0/1:52,16:68:64:64,0,1101 0/0:68,13:81:99:0,99,1505 0/0:41,8:49:51:0,51,1010 0/1:40,9:49:21:21,0,702 0/1:38,19:58:99:153,0,760
147
+ 1 16103 . T G 2348.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-1.646;DP=526;Dels=0.00;FS=2.577;HaplotypeScore=0.9645;MLEAC=7;MLEAF=0.500;MQ=26.64;MQ0=82;MQRankSum=-2.736;QD=4.47;ReadPosRankSum=-2.044 GT:AD:DP:GQ:PL 0/1:21,29:50:99:504,0,450 0/1:55,24:79:99:209,0,838 0/1:49,37:86:99:456,0,1002 0/1:74,32:106:99:193,0,1519 0/1:41,19:60:99:141,0,740 0/1:38,23:61:99:257,0,548 0/1:38,46:84:99:628,0,641
data/test/data/regression/rewrite.info.sample-stderr.new ADDED
@@ -0,0 +1,4 @@
1
+ bio-vcf 0.9.0-pre2 (biogem Ruby 2.2.2 with pcows) by Pjotr Prins 2015
2
+ Waiting up to 180 seconds for pid=3668 to complete
3
+ OK pid=3668, processing /tmp/bio-vcf_20150816-3666-cjkeqc/000001-bio-vcf
4
+ Processing /tmp/bio-vcf_20150816-3666-cjkeqc/000001-bio-vcf
data/test/data/regression/rewrite.info.sample.new ADDED
@@ -0,0 +1,150 @@
1
+ ##fileformat=VCFv4.1
2
+ ##FILTER=<ID=LowQual,Description="Low quality">
3
+ ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
4
+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
5
+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
6
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
7
+ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
8
+ ##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.8-1-g932cd3a,Date="Sat Jan 25 10:33:56 CET 2014",Epoch=1390642436187,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/data_fedor12/BAM/sander/Liver_clones/BIOPSY17513D/mapping/BIOPSY17513D_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone3/mapping/clone3_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone4/mapping/clone4_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/clone10/mapping/clone10_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone33/mapping/subclone33_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone46/mapping/subclone46_dedup_realigned_recalibrated.bam, /data_fedor12/BAM/sander/Liver_clones/subclone105/mapping/subclone105_dedup_realigned_recalibrated.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/data_fedor13/sander/variant_calling/Liver_clones/.queue/scatterGather/UnifiedGenotyper_noref-1-sg/temp_001_of_500/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data_fedor13/common_data/references/H_sapiens/GATK_b37_bundle_reference/basespace/human_g1k_v37.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 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 num_threads=1 num_cpu_threads_per_data_thread=1 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=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
9
+ ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
10
+ ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
11
+ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
12
+ ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
13
+ ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
14
+ ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
15
+ ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
16
+ ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
17
+ ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
18
+ ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
19
+ ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
20
+ ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
21
+ ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
22
+ ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
23
+ ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
24
+ ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
25
+ ##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
26
+ ##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
27
+ ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
28
+ ##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
29
+ ##contig=<ID=1,length=249250621,assembly=b37>
30
+ ##contig=<ID=2,length=243199373,assembly=b37>
31
+ ##contig=<ID=3,length=198022430,assembly=b37>
32
+ ##contig=<ID=4,length=191154276,assembly=b37>
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+ ##contig=<ID=5,length=180915260,assembly=b37>
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+ ##contig=<ID=6,length=171115067,assembly=b37>
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+ ##contig=<ID=8,length=146364022,assembly=b37>
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+ ##contig=<ID=9,length=141213431,assembly=b37>
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+ ##contig=<ID=10,length=135534747,assembly=b37>
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+ ##contig=<ID=11,length=135006516,assembly=b37>
40
+ ##contig=<ID=12,length=133851895,assembly=b37>
41
+ ##contig=<ID=13,length=115169878,assembly=b37>
42
+ ##contig=<ID=14,length=107349540,assembly=b37>
43
+ ##contig=<ID=15,length=102531392,assembly=b37>
44
+ ##contig=<ID=16,length=90354753,assembly=b37>
45
+ ##contig=<ID=17,length=81195210,assembly=b37>
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+ ##contig=<ID=18,length=78077248,assembly=b37>
47
+ ##contig=<ID=19,length=59128983,assembly=b37>
48
+ ##contig=<ID=20,length=63025520,assembly=b37>
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+ ##contig=<ID=21,length=48129895,assembly=b37>
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+ ##contig=<ID=22,length=51304566,assembly=b37>
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+ ##contig=<ID=X,length=155270560,assembly=b37>
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+ ##contig=<ID=Y,length=59373566,assembly=b37>
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+ ##contig=<ID=MT,length=16569,assembly=b37>
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95
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97
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99
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100
+ ##contig=<ID=GL000215.1,length=172545,assembly=b37>
101
+ ##contig=<ID=GL000205.1,length=174588,assembly=b37>
102
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103
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104
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105
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106
+ ##contig=<ID=GL000212.1,length=186858,assembly=b37>
107
+ ##contig=<ID=GL000222.1,length=186861,assembly=b37>
108
+ ##contig=<ID=GL000200.1,length=187035,assembly=b37>
109
+ ##contig=<ID=GL000193.1,length=189789,assembly=b37>
110
+ ##contig=<ID=GL000194.1,length=191469,assembly=b37>
111
+ ##contig=<ID=GL000225.1,length=211173,assembly=b37>
112
+ ##contig=<ID=GL000192.1,length=547496,assembly=b37>
113
+ ##reference=file:human_g1k_v37.fasta
114
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2
115
+ 1 10257 . A C 77.69 . AC=1;AF=0.071;AN=14;BaseQRankSum=-0.066;DP=1518;Dels=0.00;FS=24.214;HaplotypeScore=226.5209;MLEAC=1;MLEAF=0.071;MQ=25.00;MQ0=329;MQRankSum=-1.744;QD=0.37;ReadPosRankSum=1.551;sample=XXXXX GT:AD:DP:GQ:PL 0/0:151,8:159:99:0,195,2282 0/0:219,22:242:99:0,197,2445 0/0:227,22:249:90:0,90,2339 0/0:226,22:249:99:0,159,2695 0/0:166,18:186:99:0,182,1989 0/1:185,27:212:99:111,0,2387 0/0:201,15:218:24:0,24,1972
116
+ 1 10291 . C T 1031.89 . AC=7;AF=0.500;AN=14;BaseQRankSum=4.367;DP=1433;Dels=0.00;FS=0.696;HaplotypeScore=101.0885;MLEAC=7;MLEAF=0.500;MQ=26.96;MQ0=225;MQRankSum=0.087;QD=0.72;ReadPosRankSum=-1.640;sample=XXXXX GT:AD:DP:GQ:PL 0/1:145,16:165:23:23,0,491 0/1:218,26:249:29:29,0,611 0/1:214,30:249:99:145,0,801 0/1:213,32:247:20:20,0,1031 0/1:122,36:161:99:347,0,182 0/1:131,27:163:99:255,0,508 0/1:156,31:189:99:252,0,372
117
+ 1 10297 . C T 187.21 . AC=5;AF=0.357;AN=14;BaseQRankSum=-2.778;DP=1440;Dels=0.00;FS=0.000;HaplotypeScore=123.6373;MLEAC=5;MLEAF=0.357;MQ=27.26;MQ0=217;MQRankSum=-2.914;QD=0.18;ReadPosRankSum=1.927;sample=XXXXX GT:AD:DP:GQ:PL 0/1:155,18:182:44:44,0,654 0/1:218,23:246:21:21,0,673 0/1:219,26:250:41:41,0,898 0/0:207,30:246:39:0,39,963 0/0:137,20:165:21:0,21,363 0/1:124,27:158:65:65,0,435 0/1:151,27:183:63:63,0,485
118
+ 1 10303 . C T 166.50 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.960;DP=1460;Dels=0.00;FS=2.121;HaplotypeScore=138.0883;MLEAC=2;MLEAF=0.143;MQ=27.29;MQ0=220;MQRankSum=-2.873;QD=0.27;ReadPosRankSum=1.756;sample=XXXXX GT:AD:DP:GQ:PL 0/1:169,25:198:99:195,0,609 0/1:211,31:247:1:1,0,656 0/0:214,28:248:7:0,7,982 0/0:214,32:248:25:0,25,980 0/0:146,17:172:2:0,2,353 0/1:123,23:157:17:17,0,541 0/0:156,22:182:19:0,19,413
119
+ 1 10315 . C T 108.20 . AC=3;AF=0.214;AN=14;BaseQRankSum=-3.769;DP=1500;Dels=0.01;FS=1.493;HaplotypeScore=169.3933;MLEAC=3;MLEAF=0.214;MQ=26.95;MQ0=241;MQRankSum=-4.511;QD=0.19;ReadPosRankSum=2.373;sample=XXXXX GT:AD:DP:GQ:PL 0/1:181,26:212:41:41,0,618 0/0:223,17:246:99:0,102,832 0/0:219,20:242:66:0,66,924 0/0:217,23:245:99:0,109,1384 0/1:155,27:190:97:97,0,328 0/1:130,20:157:10:10,0,531 0/0:163,24:189:5:0,5,450
120
+ 1 10321 . C T 106.30 . AC=5;AF=0.357;AN=14;BaseQRankSum=3.045;DP=1537;Dels=0.01;FS=5.835;HaplotypeScore=220.1531;MLEAC=5;MLEAF=0.357;MQ=26.69;MQ0=258;MQRankSum=-4.870;QD=0.10;ReadPosRankSum=0.815;sample=XXXXX GT:AD:DP:GQ:PL 0/1:189,25:218:30:30,0,810 0/0:219,22:246:24:0,24,593 0/1:218,27:248:34:34,0,1134 0/0:220,22:248:56:0,56,1207 0/1:168,23:193:19:19,0,493 0/1:139,22:164:46:46,0,689 0/1:167,26:196:20:20,0,522
121
+ 1 10327 . T C 1215.15 . AC=7;AF=0.500;AN=14;BaseQRankSum=3.585;DP=1641;Dels=0.02;FS=6.639;HaplotypeScore=237.4339;MLEAC=7;MLEAF=0.500;MQ=25.22;MQ0=321;MQRankSum=4.402;QD=0.74;ReadPosRankSum=3.957;sample=XXXXX GT:AD:DP:GQ:PL 0/1:178,56:237:99:178,0,848 0/1:178,60:238:99:320,0,575 0/1:185,40:229:99:236,0,679 0/1:184,52:237:99:358,0,544 0/1:165,43:209:57:57,0,726 0/1:151,31:183:9:9,0,780 0/1:164,46:210:96:96,0,550
122
+ 1 10583 . G A 699.85 . AC=7;AF=0.500;AN=14;BaseQRankSum=-4.714;DP=129;Dels=0.00;FS=7.556;HaplotypeScore=0.6677;MLEAC=7;MLEAF=0.500;MQ=41.33;MQ0=2;MQRankSum=-2.309;QD=5.43;ReadPosRankSum=-0.296;sample=XXXXX GT:AD:DP:GQ:PL 0/1:5,3:8:58:58,0,133 0/1:12,12:24:99:231,0,287 0/1:16,4:21:38:38,0,491 0/1:19,4:23:57:57,0,494 0/1:9,6:15:99:140,0,180 0/1:11,8:19:99:173,0,235 0/1:15,4:19:42:42,0,344
123
+ 1 10665 . C G 56.61 . AC=2;AF=0.250;AN=8;BaseQRankSum=2.219;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=25.41;MQ0=15;MQRankSum=0.185;QD=4.72;ReadPosRankSum=1.849;sample=XXXXX GT:AD:DP:GQ:PL ./. ./. 0/1:4,3:7:57:57,0,78 0/1:3,2:5:23:30,0,23 ./. 0/0:2,0:2:3:0,3,26 0/0:6,1:7:6:0,6,49
124
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125
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126
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127
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128
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129
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130
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131
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132
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133
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134
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135
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136
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137
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138
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139
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140
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141
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142
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143
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144
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145
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146
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147
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148
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149
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150
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