bio-vcf 0.8.2 → 0.9.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
@@ -0,0 +1 @@
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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
@@ -0,0 +1 @@
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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
@@ -0,0 +1 @@
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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">
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">
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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">
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">
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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>
64
+ ##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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