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##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##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">
##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">
##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">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/all.novoalign.rg.sorted.realigned.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa nonDeterministicRandomSeed=false disableRandomization=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 performanceLog=null useOriginalQualities=false 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 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=20 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 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=ORIGINAL min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 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 heterozygosity=0.0010 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY 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 contamination_fraction_to_filter=0.05 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT logRemovedReadsFromContaminationFiltering=null 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 debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##reference=file:///home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
##bcftools_viewVersion=1.1-82-g4f3a265+htslib-1.1-87-g3c4f33a
##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
##INFO=<ID=OLD_VARIANT,Number=1,Type=String,Description="Original chr:pos:ref:alt encoding">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B C D E F G H I J K L
chr1 13273 . G C 1685.64 . AC=5;AF=0.208;AN=24;BaseQRankSum=-1.06;DP=701;Dels=0;FS=0.887;HaplotypeScore=1.5983;InbreedingCoeff=-0.2652;MLEAC=5;MLEAF=0.208;MQ=25.13;MQ0=20;MQRankSum=6.545;QD=6.99;ReadPosRankSum=1.826 GT:AD:DP:GQ:PL 0/1:44,29:70:99:561,0,317 0/0:56,0:56:99:0,99,1176 0/0:158,0:158:99:0,280,3426 0/0:91,2:91:78:0,78,892 0/1:28,12:38:99:282,0,254 0/1:41,17:56:99:360,0,494 0/0:35,0:35:48:0,48,572 0/0:47,0:47:42:0,42,491 0/0:21,0:21:15:0,15,150 0/1:18,6:23:99:137,0,171 0/0:47,1:47:66:0,66,748 0/1:30,16:44:99:401,0,154
chr1 13656 . CAG C 1065.21 . AC=10;AF=0.5;AN=20;BaseQRankSum=3.156;DP=227;FS=0;InbreedingCoeff=-0.9974;MLEAC=10;MLEAF=0.5;MQ=15.83;MQ0=0;MQRankSum=2.299;QD=2.45;ReadPosRankSum=1.342 GT:AD:DP:GQ:PL 0/1:5,3:9:99:142,0,251 0/1:6,1:7:34:34,0,311 0/1:16,2:18:57:57,0,803 0/1:5,8:13:99:404,0,238 0/1:2,1:5:46:46,0,51 0/1:1,4:5:19:207,0,19 0/1:2,2:4:77:99,0,77 0/1:1,1:2:49:49,0,49 ./.:.:.:.:. ./.:.:.:.:. 0/1:2,1:3:46:46,0,102 0/1:5,1:6:37:37,0,259
chr1 14464 . A T 7711.47 . AC=7;AF=0.292;AN=24;BaseQRankSum=-0.671;DP=1873;Dels=0;FS=8.549;HaplotypeScore=3.6331;InbreedingCoeff=-0.4118;MLEAC=7;MLEAF=0.292;MQ=28.21;MQ0=70;MQRankSum=12.577;QD=6.92;ReadPosRankSum=4.608 GT:AD:DP:GQ:PL 0/0:245,5:239:99:0,247,2833 0/1:198,51:238:99:744,0,2519 0/1:106,144:238:99:3261,0,959 0/0:227,3:222:99:0,184,2148 0/0:105,1:103:99:0,159,1940 0/1:163,50:203:99:898,0,1851 0/1:64,36:95:99:842,0,192 0/1:47,67:109:45:1397,0,45 0/1:46,6:50:99:103,0,137 0/0:79,3:79:99:0,105,1241 0/1:103,33:130:99:525,0,1103 0/0:90,0:90:69:0,69,840
chr1 14653 . C T 5639.59 . AC=12;AF=0.5;AN=24;BaseQRankSum=8.24;DP=2657;Dels=0;FS=311.609;HaplotypeScore=2.3028;InbreedingCoeff=-1;MLEAC=12;MLEAF=0.5;MQ=28.88;MQ0=22;MQRankSum=2.317;QD=2.12;ReadPosRankSum=-0.665 GT:AD:DP:GQ:PL 0/1:184,66:238:99:1119,0,3133 0/1:208,42:238:99:438,0,4373 0/1:219,31:238:87:87,0,5113 0/1:194,56:238:99:583,0,3872 0/1:211,37:236:99:383,0,3687 0/1:210,40:238:99:125,0,4458 0/1:142,46:179:99:755,0,1869 0/1:216,34:238:88:88,0,3878 0/1:77,66:136:63:1649,0,63 0/1:126,26:145:99:201,0,2385 0/1:210,40:238:99:161,0,3825 0/1:154,22:168:99:103,0,2315
chr1 14907 . A G 31850.9 . AC=11;AF=0.458;AN=24;BaseQRankSum=3.666;DP=2992;Dels=0;FS=17.089;HaplotypeScore=3.5152;InbreedingCoeff=-0.8462;MLEAC=11;MLEAF=0.458;MQ=44.71;MQ0=23;MQRankSum=-1.503;QD=11.62;ReadPosRankSum=6.988 GT:AD:DP:GQ:PL 0/1:113,135:236:99:3658,0,2804 0/1:170,80:238:99:1456,0,4749 0/0:218,32:238:65:0,65,6850 0/1:129,120:237:99:3479,0,2750 0/1:82,168:238:99:5081,0,1536 0/1:161,88:237:99:2326,0,4131 0/1:137,113:238:99:3063,0,3536 0/1:120,129:243:99:3505,0,3157 0/1:149,101:238:99:2614,0,3510 0/1:144,106:238:99:2902,0,3511 0/1:207,43:238:99:444,0,5850 0/1:120,127:241:99:3378,0,3064
chr1 724714 . A T 119.73 . AC=6;AF=0.5;AN=12;BaseQRankSum=-0.529;DP=13;Dels=0;FS=0;HaplotypeScore=0.4999;MLEAC=6;MLEAF=0.5;MQ=52.23;MQ0=0;MQRankSum=0.38;QD=17.1;ReadPosRankSum=-1.309 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 ./.:.:.:.:. 0/0:4,0:4:6:0,6,90 0/1:1,1:2:36:36,0,36 1/1:0,1:1:3:39,3,0 ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 0/1:1,1:2:35:36,0,35 0/0:1,0:1:3:0,3,42
chr1 724728 . T A 168.12 . AC=7;AF=0.7;AN=10;BaseQRankSum=-1.067;DP=9;Dels=0;FS=3.332;HaplotypeScore=0.3999;MLEAC=7;MLEAF=0.7;MQ=57.14;MQ0=0;MQRankSum=-1.589;QD=24.02;ReadPosRankSum=1.067 GT:AD:DP:GQ:PL 1/1:0,2:2:3:45,3,0 ./.:.:.:.:. ./.:.:.:.:. 1/1:0,2:2:6:80,6,0 1/1:0,1:1:3:39,3,0 ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 0/1:1,1:2:34:36,0,34 0/0:1,0:1:3:0,3,42
chr1 724748 . A T 53.58 . AC=4;AF=0.5;AN=8;BaseQRankSum=-0.358;DP=6;Dels=0;FS=0;HaplotypeScore=0.25;MLEAC=4;MLEAF=0.5;MQ=59.23;MQ0=0;MQRankSum=-0.358;QD=17.86;ReadPosRankSum=0.358 GT:AD:DP:GQ:PL 1/1:0,2:2:3:41,3,0 ./.:.:.:.:. ./.:.:.:.:. 0/0:1,0:1:3:0,3,41 ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. 1/1:0,1:1:3:42,3,0 0/0:1,0:1:3:0,3,42
chr1 724749 . A T 53.58 . AC=4;AF=0.5;AN=8;BaseQRankSum=-0.358;DP=6;Dels=0;FS=0;HaplotypeScore=0.25;MLEAC=4;MLEAF=0.5;MQ=59.23;MQ0=0;MQRankSum=-0.358;QD=17.86;ReadPosRankSum=0.358 GT:AD:DP:GQ:PL ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:. ./.:.:.:.:.
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