bio-vcf 0.8.1 → 0.9.5

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Files changed (84) hide show
  1. checksums.yaml +5 -5
  2. data/.travis.yml +1 -11
  3. data/Gemfile +2 -8
  4. data/LICENSE.txt +1 -1
  5. data/README.md +467 -129
  6. data/RELEASE_NOTES.md +27 -0
  7. data/RELEASE_NOTES.md~ +11 -0
  8. data/Rakefile +9 -42
  9. data/TAGS +115 -0
  10. data/VERSION +1 -1
  11. data/bin/bio-vcf +156 -108
  12. data/bio-vcf.gemspec +13 -75
  13. data/features/cli.feature +22 -4
  14. data/features/diff_count.feature +0 -1
  15. data/features/filter.feature +12 -0
  16. data/features/multisample.feature +12 -0
  17. data/features/somaticsniper.feature +2 -0
  18. data/features/step_definitions/cli-feature.rb +15 -6
  19. data/features/step_definitions/diff_count.rb +1 -1
  20. data/features/step_definitions/multisample.rb +19 -0
  21. data/features/step_definitions/somaticsniper.rb +9 -1
  22. data/features/step_definitions/vcf_header.rb +48 -0
  23. data/features/support/env.rb +1 -11
  24. data/features/vcf_header.feature +35 -0
  25. data/lib/bio-vcf.rb +1 -0
  26. data/lib/bio-vcf/pcows.rb +303 -0
  27. data/lib/bio-vcf/vcffile.rb +46 -0
  28. data/lib/bio-vcf/vcfgenotypefield.rb +19 -19
  29. data/lib/bio-vcf/vcfheader.rb +137 -5
  30. data/lib/bio-vcf/vcfheader_line.rb +778 -0
  31. data/lib/bio-vcf/vcfrecord.rb +56 -18
  32. data/lib/bio-vcf/vcfsample.rb +26 -2
  33. data/lib/regressiontest.rb +11 -0
  34. data/lib/regressiontest/cli_exec.rb +101 -0
  35. data/ragel/gen_vcfheaderline_parser.rl +165 -0
  36. data/ragel/generate.sh +8 -0
  37. data/template/vcf2json.erb +16 -16
  38. data/template/vcf2json_full_header.erb +22 -0
  39. data/template/vcf2json_use_meta.erb +41 -0
  40. data/test/data/input/empty.vcf +2 -0
  41. data/test/data/input/gatk_exome.vcf +237 -0
  42. data/test/data/input/gatk_wgs.vcf +1000 -0
  43. data/test/data/input/test.bed +632 -0
  44. data/test/data/regression/empty-stderr.new +12 -0
  45. data/test/data/regression/empty.new +2 -0
  46. data/test/data/regression/empty.ref +2 -0
  47. data/test/data/regression/eval_once-stderr.new +2 -0
  48. data/test/data/regression/eval_once.new +1 -0
  49. data/test/data/regression/eval_once.ref +1 -0
  50. data/test/data/regression/eval_r.info.dp-stderr.new +10 -0
  51. data/test/data/regression/eval_r.info.dp.new +150 -0
  52. data/test/data/regression/ifilter_s.dp-stderr.new +34 -0
  53. data/test/data/regression/ifilter_s.dp.new +31 -0
  54. data/test/data/regression/pass1-stderr.new +10 -0
  55. data/test/data/regression/pass1.new +88 -0
  56. data/test/data/regression/pass1.ref +88 -0
  57. data/test/data/regression/r.info.dp-stderr.new +4 -0
  58. data/test/data/regression/r.info.dp.new +114 -0
  59. data/test/data/regression/rewrite.info.sample-stderr.new +10 -0
  60. data/test/data/regression/rewrite.info.sample.new +150 -0
  61. data/test/data/regression/s.dp-stderr.new +18 -0
  62. data/test/data/regression/s.dp.new +145 -0
  63. data/test/data/regression/seval_s.dp-stderr.new +10 -0
  64. data/test/data/regression/seval_s.dp.new +36 -0
  65. data/test/data/regression/sfilter_seval_s.dp-stderr.new +18 -0
  66. data/test/data/regression/sfilter_seval_s.dp.new +31 -0
  67. data/test/data/regression/thread4-stderr.new +10 -0
  68. data/test/data/regression/thread4.new +150 -0
  69. data/test/data/regression/thread4_4-stderr.new +25 -0
  70. data/test/data/regression/thread4_4.new +130 -0
  71. data/test/data/regression/thread4_4_failed_filter-stderr.new +5 -0
  72. data/test/data/regression/thread4_4_failed_filter-stderr.ref +5 -2
  73. data/test/data/regression/thread4_4_failed_filter.new +110 -0
  74. data/test/data/regression/vcf2json_full_header-stderr.new +10 -0
  75. data/test/data/regression/vcf2json_full_header.new +225 -0
  76. data/test/data/regression/vcf2json_full_header.ref +225 -0
  77. data/test/data/regression/vcf2json_use_meta-stderr.new +10 -0
  78. data/test/data/regression/vcf2json_use_meta.new +4697 -0
  79. data/test/data/regression/vcf2json_use_meta.ref +4697 -0
  80. data/test/performance/metrics.md +18 -1
  81. data/test/stress/stress_test.sh +15 -0
  82. data/test/tmp/test.vcf +12469 -0
  83. metadata +63 -64
  84. data/Gemfile.lock +0 -81
@@ -0,0 +1,12 @@
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+ bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
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+ Options: {:show_help=>false, :source=>"https://github.com/pjotrp/bioruby-vcf", :version=>"0.9.4 (Pjotr Prins)", :date=>"2020-12-22 11:30:38 +0000", :thread_lines=>40000, :timeout=>5}
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+ Waiting up to 5 seconds for pid=30726 to complete /tmp/bio-vcf_20201222-30724-19xxgvd/000001-bio-vcf
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+ OK pid=30726, processing starts of /tmp/bio-vcf_20201222-30724-19xxgvd/000001-bio-vcf
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+ Processing remaining output...
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+ Trying: [[30726, 1, "/tmp/bio-vcf_20201222-30724-19xxgvd/000001-bio-vcf"]]
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+ Set lock on [[30726, 1, "/tmp/bio-vcf_20201222-30724-19xxgvd/000001-bio-vcf"]]
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+ Processing output file /tmp/bio-vcf_20201222-30724-19xxgvd/000001-bio-vcf (blocking)
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+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30724-19xxgvd/000001-bio-vcf
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+ Trying to remove /tmp/bio-vcf_20201222-30724-19xxgvd/000001-bio-vcf.keep
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+ Removing /tmp/bio-vcf_20201222-30724-19xxgvd/000001-bio-vcf.keep
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+ Removing dir /tmp/bio-vcf_20201222-30724-19xxgvd
@@ -0,0 +1,2 @@
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+ ##fileformat=VCFv4.0
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+ #CHROM POS ID REF ALT QUAL FILTER INFO
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+ ##fileformat=VCFv4.0
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+ #CHROM POS ID REF ALT QUAL FILTER INFO
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+ bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
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+ Removing dir /tmp/bio-vcf_20201222-30676-128vka8
@@ -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"}}
@@ -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"}}
@@ -0,0 +1,10 @@
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+ bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
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+ Waiting up to 180 seconds for pid=30642 to complete /tmp/bio-vcf_20201222-30640-gf6uns/000001-bio-vcf
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+ Processing remaining output...
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+ Trying: [[30642, 1, "/tmp/bio-vcf_20201222-30640-gf6uns/000001-bio-vcf"]]
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+ Set lock on [[30642, 1, "/tmp/bio-vcf_20201222-30640-gf6uns/000001-bio-vcf"]]
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+ Processing output file /tmp/bio-vcf_20201222-30640-gf6uns/000001-bio-vcf (blocking)
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+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30640-gf6uns/000001-bio-vcf
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+ Trying to remove /tmp/bio-vcf_20201222-30640-gf6uns/000001-bio-vcf.keep
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+ Removing /tmp/bio-vcf_20201222-30640-gf6uns/000001-bio-vcf.keep
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+ Removing dir /tmp/bio-vcf_20201222-30640-gf6uns
@@ -0,0 +1,150 @@
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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">
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>
55
+ ##contig=<ID=GL000226.1,length=15008,assembly=b37>
56
+ ##contig=<ID=GL000229.1,length=19913,assembly=b37>
57
+ ##contig=<ID=GL000231.1,length=27386,assembly=b37>
58
+ ##contig=<ID=GL000210.1,length=27682,assembly=b37>
59
+ ##contig=<ID=GL000239.1,length=33824,assembly=b37>
60
+ ##contig=<ID=GL000235.1,length=34474,assembly=b37>
61
+ ##contig=<ID=GL000201.1,length=36148,assembly=b37>
62
+ ##contig=<ID=GL000247.1,length=36422,assembly=b37>
63
+ ##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
@@ -0,0 +1,34 @@
1
+ bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
2
+ Waiting up to 180 seconds for pid=30633 to complete /tmp/bio-vcf_20201222-30631-1lij1nd/000001-bio-vcf
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
+ Processing remaining output...
28
+ Trying: [[30633, 1, "/tmp/bio-vcf_20201222-30631-1lij1nd/000001-bio-vcf"]]
29
+ Set lock on [[30633, 1, "/tmp/bio-vcf_20201222-30631-1lij1nd/000001-bio-vcf"]]
30
+ Processing output file /tmp/bio-vcf_20201222-30631-1lij1nd/000001-bio-vcf (blocking)
31
+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30631-1lij1nd/000001-bio-vcf
32
+ Trying to remove /tmp/bio-vcf_20201222-30631-1lij1nd/000001-bio-vcf.keep
33
+ Removing /tmp/bio-vcf_20201222-30631-1lij1nd/000001-bio-vcf.keep
34
+ Removing dir /tmp/bio-vcf_20201222-30631-1lij1nd
@@ -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
@@ -0,0 +1,10 @@
1
+ bio-vcf 0.9.4 (biogem Ruby 2.5.5 with pcows) by Pjotr Prins 2015-2020
2
+ Waiting up to 180 seconds for pid=30735 to complete /tmp/bio-vcf_20201222-30733-1xa4emu/000001-bio-vcf
3
+ Processing remaining output...
4
+ Trying: [[30735, 1, "/tmp/bio-vcf_20201222-30733-1xa4emu/000001-bio-vcf"]]
5
+ Set lock on [[30735, 1, "/tmp/bio-vcf_20201222-30733-1xa4emu/000001-bio-vcf"]]
6
+ Processing output file /tmp/bio-vcf_20201222-30733-1xa4emu/000001-bio-vcf (blocking)
7
+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30733-1xa4emu/000001-bio-vcf
8
+ Trying to remove /tmp/bio-vcf_20201222-30733-1xa4emu/000001-bio-vcf.keep
9
+ Removing /tmp/bio-vcf_20201222-30733-1xa4emu/000001-bio-vcf.keep
10
+ Removing dir /tmp/bio-vcf_20201222-30733-1xa4emu
@@ -0,0 +1,88 @@
1
+ ##fileformat=VCFv4.1
2
+ ##fileDate=20140121
3
+ ##phasing=none
4
+ ##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta
5
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
6
+ ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
7
+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
8
+ ##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
9
+ ##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
10
+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
11
+ ##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
12
+ ##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
13
+ ##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
14
+ ##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
15
+ ##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
16
+ ##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
17
+ ##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
18
+ ##FILTER=<ID=PASS,Description="r.normal.dp>5 and r.tumor.dp>7">
19
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
20
+ 1 1636394 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:17:12,5,0,0:0,17,0,0:75:36:0:56:37:37:0:. 0/1:0/1:6:3,1,1,1:0,4,0,2:29:36:29:60,60:37:37,37:2:36
21
+ 1 36217006 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:21:9,12,0,0:0,21,0,0:90:31:0:60:37:37:0:. 0/1:0/1:6:2,2,0,2:0,4,0,2:24:31:24:60,53:37:37,37:2:31
22
+ 1 46527674 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:6,3,0,0:0,0,9,0:54:37:0:60:37:37:0:. 0/1:0/1:4:2,0,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:34
23
+ 1 108417572 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,7,0,0:48:42:0:41:37:37:0:. 0/1:0/1:4:2,0,1,1:0,2,0,2:30:42:35:60,60:37:37,37:2:31
24
+ 1 155170305 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:5,4,0,0:0,9,0,0:54:34:0:59:37:37:0:. 0/1:0/1:6:3,1,2,0:0,4,0,2:27:34:27:44,60:37:37,37:2:32
25
+ 1 155449089 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:5,4,0,0:0,0,9,0:54:37:0:60:37:37:0:. 0/1:0/1:4:1,1,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:34
26
+ 1 169847826 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:6,3,0,0:0,0,9,0:54:37:0:60:37:37:0:. 0/1:0/1:4:2,0,2,0:2,0,2,0:30:37:30:60,60:37:37,37:2:34
27
+ 1 203098164 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:3,7,0,0:0,10,0,0:57:40:0:53:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,60:37:37,37:2:37
28
+ 2 39213209 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:16:8,8,0,0:0,0,16,0:75:42:0:56:37:37:0:. 0/1:0/1:4:2,0,1,1:2,0,2,0:30:42:35:60,59:37:37,37:2:42
29
+ 2 86691250 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:6,2,0,0:0,0,8,0:51:42:0:59:37:37:0:. 0/1:0/1:4:2,0,1,1:2,0,2,0:30:42:35:60,60:37:37,37:2:33
30
+ 2 88874243 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:17:12,5,0,0:0,0,17,0:78:34:0:59:37:37:0:. 0/1:0/1:5:2,1,0,2:2,0,3,0:27:34:27:60,60:37:37,37:2:34
31
+ 2 121728044 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:6,3,0,0:0,0,9,0:54:42:0:55:37:37:0:. 0/1:0/1:4:1,1,1,1:2,0,2,0:35:42:35:60,57:37:37,37:2:36
32
+ 2 170062591 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:4,5,0,0:0,0,9,0:54:39:0:60:37:37:0:. 0/1:0/1:5:2,1,1,1:2,0,3,0:32:39:32:60,60:37:37,37:2:35
33
+ 2 216257844 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:2,5,0,0:0,0,7,0:48:40:0:60:37:37:0:. 0/1:0/1:3:1,0,0,2:2,0,1,0:1:40:33:60,60:37:37,37:2:30
34
+ 2 222322623 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:15:6,9,0,0:0,15,0,0:72:33:0:60:37:37:0:. 0/1:0/1:7:4,1,1,1:0,5,0,2:26:33:26:60,60:37:37,37:2:33
35
+ 3 25675413 . A T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:6,2,0,0:8,0,0,0:51:32:0:59:37:37:0:. 0/1:0/1:4:1,1,0,2:2,0,0,2:6:32:25:34,37:37:37,37:2:30
36
+ 3 36779638 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:13:8,5,0,0:0,13,0,0:66:36:0:60:37:37:0:. 0/1:0/1:6:1,3,1,1:0,4,0,2:29:36:29:60,60:37:37,37:2:36
37
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@@ -0,0 +1,88 @@
1
+ ##fileformat=VCFv4.1
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+ ##fileDate=20140121
3
+ ##phasing=none
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+ ##reference=file:///data/GENOMES/human_GATK_GRCh37/GRCh37_gatk.fasta
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+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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+ ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
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+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
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+ ##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
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+ ##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
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+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
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+ ##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
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+ ##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
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+ ##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
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+ ##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
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+ ##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
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+ ##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
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+ ##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
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+ ##FILTER=<ID=PASS,Description="r.normal.dp>5 and r.tumor.dp>7">
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+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
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