bio-vcf 0.8.0 → 0.9.4
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- checksums.yaml +5 -5
- data/.travis.yml +1 -11
- data/Gemfile +4 -5
- data/Gemfile.lock +28 -65
- data/LICENSE.txt +1 -1
- data/README.md +387 -107
- data/RELEASE_NOTES.md +20 -0
- data/RELEASE_NOTES.md~ +11 -0
- data/Rakefile +3 -40
- data/TAGS +115 -0
- data/VERSION +1 -1
- data/bin/bio-vcf +176 -109
- data/bio-vcf.gemspec +14 -70
- data/features/cli.feature +22 -4
- data/features/diff_count.feature +0 -1
- data/features/filter.feature +12 -0
- data/features/multisample.feature +25 -0
- data/features/somaticsniper.feature +2 -0
- data/features/step_definitions/cli-feature.rb +15 -6
- data/features/step_definitions/diff_count.rb +1 -1
- data/features/step_definitions/multisample.rb +19 -0
- data/features/step_definitions/somaticsniper.rb +9 -1
- data/features/step_definitions/vcf_header.rb +48 -0
- data/features/support/env.rb +0 -9
- data/features/vcf_header.feature +35 -0
- data/lib/bio-vcf.rb +2 -0
- data/lib/bio-vcf/bedfilter.rb +43 -0
- data/lib/bio-vcf/pcows.rb +303 -0
- data/lib/bio-vcf/template.rb +75 -0
- data/lib/bio-vcf/vcffile.rb +46 -0
- data/lib/bio-vcf/vcfgenotypefield.rb +25 -20
- data/lib/bio-vcf/vcfheader.rb +146 -6
- data/lib/bio-vcf/vcfheader_line.rb +778 -0
- data/lib/bio-vcf/vcfrecord.rb +56 -18
- data/lib/bio-vcf/vcfsample.rb +27 -3
- data/ragel/gen_vcfheaderline_parser.rl +165 -0
- data/ragel/generate.sh +8 -0
- data/template/vcf2json.erb +19 -7
- data/template/vcf2json_full_header.erb +22 -0
- data/template/vcf2json_use_meta.erb +41 -0
- data/template/vcf2rdf_header.erb +24 -0
- data/test/data/input/empty.vcf +2 -0
- data/test/data/input/gatk_exome.vcf +237 -0
- data/test/data/input/gatk_wgs.vcf +1000 -0
- data/test/data/input/test.bed +632 -0
- data/test/data/regression/empty-stderr.new +12 -0
- data/test/data/regression/empty.new +2 -0
- data/test/data/regression/empty.ref +2 -0
- data/test/data/regression/eval_once-stderr.new +2 -0
- data/test/data/regression/eval_once.new +1 -0
- data/test/data/regression/eval_once.ref +1 -0
- data/test/data/regression/eval_r.info.dp-stderr.new +10 -0
- data/test/data/regression/eval_r.info.dp.new +150 -0
- data/test/data/regression/ifilter_s.dp-stderr.new +34 -0
- data/test/data/regression/ifilter_s.dp.new +31 -0
- data/test/data/regression/pass1-stderr.new +10 -0
- data/test/data/regression/pass1.new +88 -0
- data/test/data/regression/pass1.ref +88 -0
- data/test/data/regression/r.info.dp-stderr.new +4 -0
- data/test/data/regression/r.info.dp.new +114 -0
- data/test/data/regression/rewrite.info.sample-stderr.new +10 -0
- data/test/data/regression/rewrite.info.sample.new +150 -0
- data/test/data/regression/s.dp-stderr.new +18 -0
- data/test/data/regression/s.dp.new +145 -0
- data/test/data/regression/seval_s.dp-stderr.new +10 -0
- data/test/data/regression/seval_s.dp.new +36 -0
- data/test/data/regression/sfilter_seval_s.dp-stderr.new +18 -0
- data/test/data/regression/sfilter_seval_s.dp.new +31 -0
- data/test/data/regression/thread4-stderr.new +10 -0
- data/test/data/regression/thread4.new +150 -0
- data/test/data/regression/thread4_4-stderr.new +25 -0
- data/test/data/regression/thread4_4.new +130 -0
- data/test/data/regression/thread4_4_failed_filter-stderr.new +5 -0
- data/test/data/regression/thread4_4_failed_filter-stderr.ref +5 -1
- data/test/data/regression/thread4_4_failed_filter.new +110 -0
- data/test/data/regression/vcf2json_full_header-stderr.new +10 -0
- data/test/data/regression/vcf2json_full_header.new +225 -0
- data/test/data/regression/vcf2json_full_header.ref +225 -0
- data/test/data/regression/vcf2json_use_meta-stderr.new +10 -0
- data/test/data/regression/vcf2json_use_meta.new +4697 -0
- data/test/data/regression/vcf2json_use_meta.ref +4697 -0
- data/test/performance/metrics.md +18 -1
- data/test/stress/stress_test.sh +15 -0
- data/test/tmp/test.vcf +12469 -0
- metadata +65 -64
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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
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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"}}
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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"}}
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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
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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">
|
|
20
|
+
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
|
|
21
|
+
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
|
|
22
|
+
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
|
|
23
|
+
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
|
|
24
|
+
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
|
|
25
|
+
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
|
|
26
|
+
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
|
|
27
|
+
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
|
|
28
|
+
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
|
|
29
|
+
##contig=<ID=1,length=249250621,assembly=b37>
|
|
30
|
+
##contig=<ID=2,length=243199373,assembly=b37>
|
|
31
|
+
##contig=<ID=3,length=198022430,assembly=b37>
|
|
32
|
+
##contig=<ID=4,length=191154276,assembly=b37>
|
|
33
|
+
##contig=<ID=5,length=180915260,assembly=b37>
|
|
34
|
+
##contig=<ID=6,length=171115067,assembly=b37>
|
|
35
|
+
##contig=<ID=7,length=159138663,assembly=b37>
|
|
36
|
+
##contig=<ID=8,length=146364022,assembly=b37>
|
|
37
|
+
##contig=<ID=9,length=141213431,assembly=b37>
|
|
38
|
+
##contig=<ID=10,length=135534747,assembly=b37>
|
|
39
|
+
##contig=<ID=11,length=135006516,assembly=b37>
|
|
40
|
+
##contig=<ID=12,length=133851895,assembly=b37>
|
|
41
|
+
##contig=<ID=13,length=115169878,assembly=b37>
|
|
42
|
+
##contig=<ID=14,length=107349540,assembly=b37>
|
|
43
|
+
##contig=<ID=15,length=102531392,assembly=b37>
|
|
44
|
+
##contig=<ID=16,length=90354753,assembly=b37>
|
|
45
|
+
##contig=<ID=17,length=81195210,assembly=b37>
|
|
46
|
+
##contig=<ID=18,length=78077248,assembly=b37>
|
|
47
|
+
##contig=<ID=19,length=59128983,assembly=b37>
|
|
48
|
+
##contig=<ID=20,length=63025520,assembly=b37>
|
|
49
|
+
##contig=<ID=21,length=48129895,assembly=b37>
|
|
50
|
+
##contig=<ID=22,length=51304566,assembly=b37>
|
|
51
|
+
##contig=<ID=X,length=155270560,assembly=b37>
|
|
52
|
+
##contig=<ID=Y,length=59373566,assembly=b37>
|
|
53
|
+
##contig=<ID=MT,length=16569,assembly=b37>
|
|
54
|
+
##contig=<ID=GL000207.1,length=4262,assembly=b37>
|
|
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
|
+
3 123458847 . T C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:4,6,0,0:0,0,0,10:54:39:0:41:37:37:0:. 0/1:0/1:5:1,2,1,1:0,2,0,3:32:39:32:55,45:37:37,37:2:35
|
|
38
|
+
3 124351308 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:7,1,0,0:0,0,8,0:51:42:0:58:37:37:0:. 0/1:0/1:4:1,1,1,1:2,0,2,0:35:42:35:60,60:37:37,37:2:33
|
|
39
|
+
3 142171996 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:8,2,0,0:0,10,0,0:57:37:0:59:37:37:0:. 0/1:0/1:4:0,2,2,0:0,2,0,2:30:37:30:60,60:37:37,37:2:35
|
|
40
|
+
3 189526168 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:23:11,12,0,0:0,0,23,0:96:36:0:59:37:37:0:. 0/1:0/1:6:1,3,1,1:2,0,4,0:29:36:29:60,60:37:37,37:2:36
|
|
41
|
+
4 82058553 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:37:0:60:37:37:0:. 0/1:0/1:4:2,0,2,0:0,2,0,2:30:37:30:60,60:37:37,37:2:30
|
|
42
|
+
4 122769998 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:7,0,0,0:0,7,0,0:48:40:0:54:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,60:37:37,37:2:30
|
|
43
|
+
5 13850856 . G C . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:3,5,0,0:0,0,8,0:51:40:0:51:37:37:0:. 0/1:0/1:3:0,1,2,0:0,2,1,0:1:40:33:49,60:37:37,37:2:33
|
|
44
|
+
5 132038609 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:12:10,2,0,0:0,12,0,0:63:33:0:58:37:37:0:. 0/1:0/1:7:3,2,1,1:0,5,0,2:26:33:26:60,60:37:37,37:2:33
|
|
45
|
+
5 137756599 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:13:7,6,0,0:0,13,0,0:66:31:0:60:37:37:0:. 0/1:0/1:6:2,2,2,0:0,4,0,2:24:31:24:60,60:37:37,37:2:31
|
|
46
|
+
5 141974902 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:9,5,0,0:0,14,0,0:69:40:0:60:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,60:37:37,37:2:40
|
|
47
|
+
6 2749400 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:8,2,0,0:0,10,0,0:57:35:0:60:37:37:0:. 0/1:0/1:4:2,0,0,2:0,2,0,2:28:35:28:60,39:37:37,37:2:34
|
|
48
|
+
7 95217113 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:36:0:60:37:37:0:. 0/1:0/1:6:1,3,1,1:2,0,4,0:29:36:29:60,60:37:37,37:2:30
|
|
49
|
+
7 140434525 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:8,6,0,0:0,0,14,0:69:31:0:59:37:37:0:. 0/1:0/1:6:3,1,0,2:2,0,4,0:24:31:24:60,58:37:37,37:2:31
|
|
50
|
+
7 151856059 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:20:9,10,1,0:0,19,0,1:50:33:0:59:37:37:0:. 0/1:0/1:7:1,4,1,1:0,5,0,2:26:33:26:60,60:37:37,37:2:30
|
|
51
|
+
8 42958817 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:12:6,6,0,0:0,12,0,0:60:36:0:55:37:37:0:. 0/1:0/1:7:4,1,1,1:0,5,0,2:29:36:29:48,60:37:37,37:2:35
|
|
52
|
+
8 131070237 . A G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:13:9,4,0,0:13,0,0,0:66:39:0:60:37:37:0:. 0/1:0/1:5:2,1,1,1:3,0,2,0:32:39:32:60,60:37:37,37:2:39
|
|
53
|
+
8 141711010 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:8,2,0,0:0,10,0,0:57:40:0:59:37:37:0:. 0/1:0/1:3:1,0,2,0:0,1,0,2:1:40:33:60,55:37:37,37:2:37
|
|
54
|
+
8 145059674 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:7,7,0,0:0,14,0,0:69:34:0:56:37:37:0:. 0/1:0/1:5:2,1,0,2:0,3,0,2:27:34:27:60,60:37:37,37:2:34
|
|
55
|
+
9 111651620 . A T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:4,3,0,0:7,0,0,0:48:92:0:60:37:37:0:. 0/1:0/1:7:1,2,3,1:3,0,0,4:58:92:85:60,60:37:37,37:2:31
|
|
56
|
+
9 111685156 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:13:9,4,0,0:0,0,13,0:66:37:0:60:37:37:0:. 0/1:0/1:4:1,1,2,0:2,0,2,0:12:37:30:60,37:37:37,37:2:37
|
|
57
|
+
10 6525571 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:0,8,0,0:0,0,8,0:51:37:0:55:37:37:0:. 0/1:0/1:4:1,1,0,2:2,0,2,0:30:37:30:60,60:37:37,37:2:32
|
|
58
|
+
10 97197246 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:7,3,0,0:0,10,0,0:57:39:0:58:37:37:0:. 0/1:0/1:5:3,0,1,1:0,3,0,2:32:39:32:60,53:37:37,37:2:36
|
|
59
|
+
11 58949455 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:12:8,4,0,0:0,0,12,0:60:33:0:54:37:37:0:. 0/1:0/1:7:3,2,1,1:2,0,5,0:26:33:26:60,36:37:37,37:2:33
|
|
60
|
+
11 65481082 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:17:12,5,0,0:0,0,17,0:78:45:0:58:37:37:0:. 0/1:0/1:3:0,1,1,1:2,0,1,0:1:45:34:60,60:37:37,37:2:45
|
|
61
|
+
11 94180424 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:23:17,6,0,0:0,0,23,0:96:34:0:56:37:37:0:. 0/1:0/1:5:2,1,2,0:2,0,3,0:27:34:27:60,59:37:37,37:2:34
|
|
62
|
+
11 121036021 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:12:3,9,0,0:0,12,0,0:63:31:0:59:37:37:0:. 0/1:0/1:6:4,0,0,2:0,4,0,2:24:31:24:59,60:37:37,37:2:31
|
|
63
|
+
12 994952 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:1,8,0,0:0,9,0,0:54:33:0:59:37:37:0:. 0/1:0/1:7:2,3,1,1:0,5,0,2:26:33:26:51,55:37:37,37:2:32
|
|
64
|
+
12 69233187 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:5,4,0,0:0,9,0,0:51:33:0:53:37:37:0:. 0/1:0/1:7:4,1,1,1:0,5,0,2:26:33:26:60,60:37:37,37:2:30
|
|
65
|
+
12 77436879 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:10:4,6,0,0:0,0,10,0:57:34:0:60:37:37:0:. 0/1:0/1:5:2,1,0,2:2,0,3,0:27:34:27:60,60:37:37,37:2:33
|
|
66
|
+
12 96641273 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:4,4,0,0:0,0,8,0:51:33:0:60:37:37:0:. 0/1:0/1:7:2,3,1,1:2,0,5,0:26:33:26:60,50:37:37,37:2:30
|
|
67
|
+
12 110813986 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:8:4,4,0,0:0,0,8,0:51:39:0:59:37:37:0:. 0/1:0/1:5:1,2,1,1:2,0,3,0:32:39:32:60,60:37:37,37:2:33
|
|
68
|
+
12 122825587 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:21:12,9,0,0:0,21,0,0:90:34:0:59:37:37:0:. 0/1:0/1:5:3,0,2,0:0,3,0,2:27:34:27:60,60:37:37,37:2:34
|
|
69
|
+
14 30135337 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,7,0,0:48:40:0:60:37:37:0:. 0/1:0/1:3:1,0,0,2:0,1,0,2:1:40:33:60,60:37:37,37:2:30
|
|
70
|
+
14 51398458 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:4,5,0,0:0,0,9,0:54:36:0:55:37:37:0:. 0/1:0/1:6:0,4,1,1:2,0,4,0:29:36:29:60,59:37:37,37:2:33
|
|
71
|
+
15 43170722 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:6,5,0,0:0,11,0,0:60:31:0:60:37:37:0:. 0/1:0/1:6:4,0,2,0:0,4,0,2:24:31:24:56,54:37:37,37:2:31
|
|
72
|
+
15 50862183 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:7,2,0,0:0,9,0,0:54:35:0:60:37:37:0:. 0/1:0/1:4:0,2,0,2:2,2,0,0:28:35:28:45,59:37:37,37:2:33
|
|
73
|
+
15 64332347 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:6,1,0,0:0,7,0,0:48:39:0:60:37:37:0:. 0/1:0/1:5:3,0,1,1:0,3,0,2:32:39:32:58,56:37:37,37:2:30
|
|
74
|
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@@ -0,0 +1,88 @@
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##fileformat=VCFv4.1
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##fileDate=20140121
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##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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8
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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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9
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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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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
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15 50862183 . C A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:9:7,2,0,0:0,9,0,0:54:35:0:60:37:37:0:. 0/1:0/1:4:0,2,0,2:2,2,0,0:28:35:28:45,59:37:37,37:2:33
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16 23619204 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:42:0:60:37:37:0:. 0/1:0/1:4:1,1,1,1:2,0,2,0:35:42:35:60,60:37:37,37:2:31
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19 39664512 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:14:8,6,0,0:0,14,0,0:69:42:0:60:37:37:0:. 0/1:0/1:4:0,2,1,1:0,2,0,2:30:42:35:60,60:37:37,37:2:42
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X 70341572 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:11:6,5,0,0:0,11,0,0:60:33:0:56:37:37:0:. 0/1:0/1:7:3,2,1,1:0,5,0,2:26:33:26:58,60:37:37,37:2:33
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X 123164862 . G A . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:7:5,2,0,0:0,0,7,0:48:40:0:59:37:37:0:. 0/1:0/1:3:1,0,2,0:2,0,1,0:1:40:33:60,60:37:37,37:2:30
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