bio-vcf 0.8.1 → 0.9.5

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 (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
data/test/data/regression/r.info.dp-stderr.new ADDED
@@ -0,0 +1,4 @@
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=31046 to complete /tmp/bio-vcf_20201222-31044-fq0sit/000001-bio-vcf
3
+ ERROR:
4
+ Removing dir /tmp/bio-vcf_20201222-31044-fq0sit
data/test/data/regression/r.info.dp.new ADDED
@@ -0,0 +1,114 @@
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>
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+ ##contig=<ID=4,length=191154276,assembly=b37>
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+ ##contig=<ID=5,length=180915260,assembly=b37>
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+ ##contig=<ID=6,length=171115067,assembly=b37>
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+ ##contig=<ID=7,length=159138663,assembly=b37>
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+ ##contig=<ID=8,length=146364022,assembly=b37>
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+ ##contig=<ID=9,length=141213431,assembly=b37>
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+ ##contig=<ID=10,length=135534747,assembly=b37>
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+ ##contig=<ID=11,length=135006516,assembly=b37>
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+ ##contig=<ID=12,length=133851895,assembly=b37>
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+ ##contig=<ID=13,length=115169878,assembly=b37>
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+ ##contig=<ID=14,length=107349540,assembly=b37>
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+ ##contig=<ID=15,length=102531392,assembly=b37>
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+ ##contig=<ID=16,length=90354753,assembly=b37>
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+ ##contig=<ID=17,length=81195210,assembly=b37>
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+ ##contig=<ID=18,length=78077248,assembly=b37>
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+ ##contig=<ID=19,length=59128983,assembly=b37>
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+ ##contig=<ID=20,length=63025520,assembly=b37>
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+ ##contig=<ID=21,length=48129895,assembly=b37>
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+ ##contig=<ID=22,length=51304566,assembly=b37>
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+ ##contig=<ID=X,length=155270560,assembly=b37>
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+ ##contig=<ID=Y,length=59373566,assembly=b37>
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+ ##contig=<ID=MT,length=16569,assembly=b37>
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+ ##contig=<ID=GL000207.1,length=4262,assembly=b37>
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+ ##contig=<ID=GL000226.1,length=15008,assembly=b37>
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+ ##contig=<ID=GL000229.1,length=19913,assembly=b37>
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+ ##contig=<ID=GL000231.1,length=27386,assembly=b37>
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+ ##contig=<ID=GL000210.1,length=27682,assembly=b37>
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+ ##contig=<ID=GL000239.1,length=33824,assembly=b37>
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+ ##contig=<ID=GL000235.1,length=34474,assembly=b37>
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+ ##contig=<ID=GL000201.1,length=36148,assembly=b37>
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+ ##contig=<ID=GL000247.1,length=36422,assembly=b37>
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+ ##contig=<ID=GL000245.1,length=36651,assembly=b37>
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+ ##contig=<ID=GL000197.1,length=37175,assembly=b37>
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+ ##contig=<ID=GL000203.1,length=37498,assembly=b37>
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+ ##contig=<ID=GL000246.1,length=38154,assembly=b37>
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+ ##contig=<ID=GL000249.1,length=38502,assembly=b37>
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+ ##contig=<ID=GL000196.1,length=38914,assembly=b37>
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+ ##contig=<ID=GL000248.1,length=39786,assembly=b37>
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+ ##contig=<ID=GL000244.1,length=39929,assembly=b37>
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+ ##contig=<ID=GL000238.1,length=39939,assembly=b37>
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+ ##contig=<ID=GL000202.1,length=40103,assembly=b37>
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+ ##contig=<ID=GL000234.1,length=40531,assembly=b37>
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+ ##contig=<ID=GL000232.1,length=40652,assembly=b37>
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+ ##contig=<ID=GL000206.1,length=41001,assembly=b37>
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+ ##contig=<ID=GL000240.1,length=41933,assembly=b37>
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+ ##contig=<ID=GL000236.1,length=41934,assembly=b37>
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+ ##contig=<ID=GL000241.1,length=42152,assembly=b37>
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+ ##contig=<ID=GL000243.1,length=43341,assembly=b37>
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+ ##contig=<ID=GL000242.1,length=43523,assembly=b37>
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+ ##contig=<ID=GL000230.1,length=43691,assembly=b37>
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+ ##contig=<ID=GL000237.1,length=45867,assembly=b37>
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+ ##contig=<ID=GL000233.1,length=45941,assembly=b37>
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+ ##contig=<ID=GL000204.1,length=81310,assembly=b37>
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+ ##contig=<ID=GL000198.1,length=90085,assembly=b37>
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+ ##contig=<ID=GL000208.1,length=92689,assembly=b37>
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+ ##contig=<ID=GL000191.1,length=106433,assembly=b37>
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+ ##contig=<ID=GL000227.1,length=128374,assembly=b37>
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+ ##contig=<ID=GL000228.1,length=129120,assembly=b37>
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+ ##contig=<ID=GL000214.1,length=137718,assembly=b37>
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+ ##contig=<ID=GL000221.1,length=155397,assembly=b37>
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+ ##contig=<ID=GL000209.1,length=159169,assembly=b37>
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+ ##contig=<ID=GL000218.1,length=161147,assembly=b37>
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+ ##contig=<ID=GL000220.1,length=161802,assembly=b37>
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+ ##contig=<ID=GL000213.1,length=164239,assembly=b37>
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+ ##contig=<ID=GL000211.1,length=166566,assembly=b37>
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+ ##contig=<ID=GL000199.1,length=169874,assembly=b37>
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+ ##contig=<ID=GL000217.1,length=172149,assembly=b37>
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+ ##contig=<ID=GL000216.1,length=172294,assembly=b37>
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+ ##contig=<ID=GL000215.1,length=172545,assembly=b37>
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+ ##contig=<ID=GL000205.1,length=174588,assembly=b37>
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+ ##contig=<ID=GL000219.1,length=179198,assembly=b37>
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+ ##contig=<ID=GL000224.1,length=179693,assembly=b37>
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+ ##contig=<ID=GL000223.1,length=180455,assembly=b37>
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+ ##contig=<ID=GL000195.1,length=182896,assembly=b37>
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+ ##contig=<ID=GL000212.1,length=186858,assembly=b37>
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+ ##contig=<ID=GL000222.1,length=186861,assembly=b37>
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+ ##contig=<ID=GL000200.1,length=187035,assembly=b37>
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+ ##contig=<ID=GL000193.1,length=189789,assembly=b37>
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+ ##contig=<ID=GL000194.1,length=191469,assembly=b37>
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+ ##contig=<ID=GL000225.1,length=211173,assembly=b37>
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+ ##contig=<ID=GL000192.1,length=547496,assembly=b37>
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+ ##reference=file:human_g1k_v37.fasta
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+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Original s1t1 s2t1 s3t1 s1t2 s2t2 s3t2
data/test/data/regression/rewrite.info.sample-stderr.new ADDED
@@ -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
2
+ Waiting up to 180 seconds for pid=30669 to complete /tmp/bio-vcf_20201222-30667-hcdvz2/000001-bio-vcf
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+ Processing remaining output...
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+ Trying: [[30669, 1, "/tmp/bio-vcf_20201222-30667-hcdvz2/000001-bio-vcf"]]
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+ Set lock on [[30669, 1, "/tmp/bio-vcf_20201222-30667-hcdvz2/000001-bio-vcf"]]
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+ Processing output file /tmp/bio-vcf_20201222-30667-hcdvz2/000001-bio-vcf (blocking)
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+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30667-hcdvz2/000001-bio-vcf
8
+ Trying to remove /tmp/bio-vcf_20201222-30667-hcdvz2/000001-bio-vcf.keep
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+ Removing /tmp/bio-vcf_20201222-30667-hcdvz2/000001-bio-vcf.keep
10
+ Removing dir /tmp/bio-vcf_20201222-30667-hcdvz2
data/test/data/regression/rewrite.info.sample.new ADDED
@@ -0,0 +1,150 @@
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+ ##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">
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+ ##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
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30
+ ##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>
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>
50
+ ##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>
53
+ ##contig=<ID=MT,length=16569,assembly=b37>
54
+ ##contig=<ID=GL000207.1,length=4262,assembly=b37>
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100
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+ ##contig=<ID=GL000205.1,length=174588,assembly=b37>
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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;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
+ 1 10694 . C G 85.78 . AC=4;AF=1.00;AN=4;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=17.21;MQ0=17;QD=8.58;sample=XXXXX GT:AD:DP:GQ:PL ./. ./. 1/1:2,3:5:6:74,6,0 1/1:3,2:5:3:35,3,0 ./. ./. ./.
125
+ 1 10723 . C G 73.85 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.300;DP=18;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=20.49;MQ0=11;MQRankSum=1.754;QD=8.21;ReadPosRankSum=0.000;sample=XXXXX GT:AD:DP:GQ:PL ./. ./. 1/1:2,2:4:6:66,6,0 1/1:4,1:5:3:36,3,0 ./. ./. 0/0:6,0:6:3:0,3,33
126
+ 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;sample=XXXXX 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
127
+ 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;sample=XXXXX 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
128
+ 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;sample=XXXXX 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
129
+ 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;sample=XXXXX 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
130
+ 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;sample=XXXXX 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
131
+ 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;sample=XXXXX 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
132
+ 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;sample=XXXXX 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
133
+ 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;sample=XXXXX 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
134
+ 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;sample=XXXXX 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
135
+ 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;sample=XXXXX 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
136
+ 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;sample=XXXXX 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
137
+ 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;sample=XXXXX 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
138
+ 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;sample=XXXXX 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
139
+ 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;sample=XXXXX 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
140
+ 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;sample=XXXXX 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
141
+ 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;sample=XXXXX 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
142
+ 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;sample=XXXXX 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
143
+ 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;sample=XXXXX 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
144
+ 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;sample=XXXXX 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
145
+ 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;sample=XXXXX 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
146
+ 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;sample=XXXXX 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
147
+ 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;sample=XXXXX 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
148
+ 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;sample=XXXXX 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
149
+ 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;sample=XXXXX 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
150
+ 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;sample=XXXXX 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/s.dp-stderr.new ADDED
@@ -0,0 +1,18 @@
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=30624 to complete /tmp/bio-vcf_20201222-30622-9czlqz/000001-bio-vcf
3
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
4
+ [:filter, "s.dp>20"]
5
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
6
+ [:filter, "s.dp>20"]
7
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
8
+ [:filter, "s.dp>20"]
9
+ [:format, {"GT"=>0, "AD"=>1, "DP"=>2, "GQ"=>3, "PL"=>4}, :sample, ["./."]]
10
+ [:filter, "s.dp>20"]
11
+ Processing remaining output...
12
+ Trying: [[30624, 1, "/tmp/bio-vcf_20201222-30622-9czlqz/000001-bio-vcf"]]
13
+ Set lock on [[30624, 1, "/tmp/bio-vcf_20201222-30622-9czlqz/000001-bio-vcf"]]
14
+ Processing output file /tmp/bio-vcf_20201222-30622-9czlqz/000001-bio-vcf (blocking)
15
+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30622-9czlqz/000001-bio-vcf
16
+ Trying to remove /tmp/bio-vcf_20201222-30622-9czlqz/000001-bio-vcf.keep
17
+ Removing /tmp/bio-vcf_20201222-30622-9czlqz/000001-bio-vcf.keep
18
+ Removing dir /tmp/bio-vcf_20201222-30622-9czlqz
data/test/data/regression/s.dp.new ADDED
@@ -0,0 +1,145 @@
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
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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=13,length=115169878,assembly=b37>
42
+ ##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>
48
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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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110
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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 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
123
+ 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
124
+ 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
125
+ 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
126
+ 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
127
+ 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
128
+ 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
129
+ 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
130
+ 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
131
+ 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
132
+ 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
133
+ 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
134
+ 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
135
+ 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
136
+ 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
137
+ 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
138
+ 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
139
+ 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
140
+ 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
141
+ 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
142
+ 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
143
+ 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
144
+ 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
145
+ 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/seval_s.dp-stderr.new ADDED
@@ -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=30651 to complete /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf
3
+ Processing remaining output...
4
+ Trying: [[30651, 1, "/tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf"]]
5
+ Set lock on [[30651, 1, "/tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf"]]
6
+ Processing output file /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf (blocking)
7
+ Checking for output_lock on existing /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf
8
+ Trying to remove /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf.keep
9
+ Removing /tmp/bio-vcf_20201222-30649-gol7rw/000001-bio-vcf.keep
10
+ Removing dir /tmp/bio-vcf_20201222-30649-gol7rw