##fileformat=VCFv4.1 ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[../Bfast_Default/brca1_18.recalib.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[BadCigar] intervals=null excludeIntervals=null reference_sequence=ref_chr17.hg19.fa rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=ERROR log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=dbsnp_132.hg19.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[]" ##contig= ##reference=file:///CL_diags/ngs/OmixonPaper/brca1-test-suite/ref_chr17.hg19.fa #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DePristo 17 19588974 . G T 6.39 LowQual AC=1;AF=0.50;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=43.89;MQ0=0;QD=3.20 GT:AD:DP:GQ:PL 0/1:0,2:2:1.76:35,3,0 17 19589026 . G T 5.72 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0000;MQ=62.00;MQ0=0;QD=5.72 GT:AD:DP:GQ:PL 0/1:0,1:1:1.76:34,3,0 17 41196309 . T TGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6823.39 PASS AC=2;AF=1.00;AN=2;DP=42;FS=0.000;HRun=2;HaplotypeScore=590.6470;MQ=30.45;MQ0=0;QD=162.46 GT:AD:DP:GQ:PL 1/1:2,2:30:87.29:6823,87,0 17 41197777 rs80357307 C T 3603.77 PASS AC=2;AF=1.00;AN=2;DB;DP=130;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=3.3999;MQ=38.55;MQ0=0;QD=27.72 GT:AD:DP:GQ:PL 1/1:2,128:130:99:3602,337,0 17 41199678 rs80356868 C A 3867 PASS AC=2;AF=1.00;AN=2;DB;DP=149;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=9.0364;MQ=44.16;MQ0=0;QD=25.95 GT:AD:DP:GQ:PL 1/1:2,146:148:99:3865,361,0 17 41201435 rs75604863 A T 4216.04 PASS AC=2;AF=1.00;AN=2;DB;DP=137;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=15.0194;MQ=42.19;MQ0=0;QD=30.77 GT:AD:DP:GQ:PL 1/1:5,132:137:99:4215,376,0 17 41203088 . ATG A 1332.79 PASS AC=2;AF=1.00;AN=2;DP=147;FS=0.000;HRun=0;HaplotypeScore=455.2107;MQ=34.05;MQ0=0;QD=9.07 GT:AD:DP:GQ:PL 1/1:125,22:69:99:1375,196,0 17 41203090 rs80357818 GTT G 3282.34 PASS AC=2;AF=1.00;AN=2;DB;DP=147;FS=0.000;HRun=2;HaplotypeScore=272.0632;MQ=34.50;MQ0=0;QD=22.33 GT:AD:DP:GQ:PL 1/1:27,120:70:99:3282,205,0 17 41218426 rs8176239 G A 2377.10 PASS AC=2;AF=1.00;AN=2;DB;DP=155;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=19.4792;MQ=27.81;MQ0=0;QD=15.34 GT:AD:DP:GQ:PL 1/1:3,150:154:99:2410,237,0 17 41226347 rs80358044 C T 4235.89 PASS AC=2;AF=1.00;AN=2;DB;DP=140;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=7.5381;MQ=40.69;MQ0=0;QD=30.26 GT:AD:DP:GQ:PL 1/1:2,136:139:99:4235,385,0 17 41226354 rs80356906 C G 4207.18 PASS AC=2;AF=1.00;AN=2;DB;DP=142;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=11.3454;MQ=40.67;MQ0=0;QD=29.63 GT:AD:DP:GQ:PL 1/1:4,138:142:99:4206,388,0 17 41230990 rs8176196 A G 1247.02 PASS AC=2;AF=1.00;AN=2;DB;DP=161;Dels=0.01;FS=0.000;HRun=2;HaplotypeScore=5.3794;MQ=15.55;MQ0=0;QD=7.75 GT:AD:DP:GQ:PL 1/1:1,156:159:99:1280,135,0 17 41234435 rs80357354 C T 4108.59 PASS AC=2;AF=1.00;AN=2;DB;DP=134;Dels=0.01;FS=0.000;HRun=3;HaplotypeScore=8.3373;MQ=48.89;MQ0=0;QD=30.66 GT:AD:DP:GQ:PL 1/1:2,129:133:99:4107,373,0 17 41234579 rs80357473 A G 3704.60 PASS AC=2;AF=1.00;AN=2;DB;DP=134;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=9.3320;MQ=46.85;MQ0=0;QD=27.65 GT:AD:DP:GQ:PL 1/1:0,133:134:99:3668,381,0 17 41238149 . AC A 1107.06 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-3.997;DP=168;FS=5.251;HRun=1;HaplotypeScore=1446.4865;MQ=36.54;MQ0=0;MQRankSum=8.554;QD=6.59;ReadPosRankSum=-5.404 GT:AD:DP:GQ:PL 0/1:132,36:151:99:1146,0,3724 17 41238152 . C CA 1768.17 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-5.185;DP=165;FS=1.340;HRun=1;HaplotypeScore=1389.6225;MQ=36.87;MQ0=0;MQRankSum=8.000;QD=10.72;ReadPosRankSum=-2.990 GT:AD:DP:GQ:PL 0/1:149,16:148:99:1807,0,572 17 41238156 . CA C 1872.16 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-8.740;DP=163;FS=3.096;HRun=1;HaplotypeScore=1390.3500;MQ=36.73;MQ0=0;MQRankSum=9.440;QD=11.49;ReadPosRankSum=-4.517 GT:AD:DP:GQ:PL 0/1:113,44:146:11.29:1911,0,11 17 41238157 rs72023429 A AACACAC 13412.12 PASS AC=2;AF=1.00;AN=2;DB;DP=163;FS=0.000;HRun=0;HaplotypeScore=685.7473;MQ=36.55;MQ0=0;QD=82.28 GT:AD:DP:GQ:PL 1/1:55,76:145:99:13412,430,0 17 41244316 . GCC G 1217.55 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=4.050;DP=149;FS=0.000;HRun=3;HaplotypeScore=576.6264;MQ=32.47;MQ0=0;MQRankSum=-1.121;QD=8.17;ReadPosRankSum=3.526 GT:AD:DP:GQ:PL 1/1:120,29:91:99:1260,120,0 17 41244321 rs80357313 C G 1358.23 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-4.190;DB;DP=152;Dels=0.00;FS=7.211;HRun=0;HaplotypeScore=116.0092;MQ=32.48;MQ0=0;MQRankSum=5.329;QD=8.94;ReadPosRankSum=0.810 GT:AD:DP:GQ:PL 0/1:96,56:152:99:1388,0,913 17 41244321 . CTG C 1273.24 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.494;DP=151;FS=0.000;HRun=0;HaplotypeScore=608.6541;MQ=32.47;MQ0=0;MQRankSum=-1.906;QD=8.43;ReadPosRankSum=4.009 GT:AD:DP:GQ:PL 1/1:99,51:92:99:1315,185,0 17 41244679 rs80357929 GA G 5480.36 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-1.628;DB;DP=142;FS=3.177;HRun=1;HaplotypeScore=407.7150;MQ=41.24;MQ0=0;MQRankSum=1.498;QD=38.59;ReadPosRankSum=1.472 GT:AD:DP:GQ:PL 1/1:1,141:135:99:5480,393,0 17 41244862 rs80357188 T A 4150.54 PASS AC=2;AF=1.00;AN=2;DB;DP=146;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=7.6132;MQ=38.79;MQ0=0;QD=28.43 GT:AD:DP:GQ:PL 1/1:0,145:146:99:4149,376,0 17 41244984 . T TGA 2797.19 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=2.397;DP=162;FS=0.000;HRun=0;HaplotypeScore=662.9603;MQ=31.45;MQ0=0;MQRankSum=-0.223;QD=17.27;ReadPosRankSum=1.900 GT:AD:DP:GQ:PL 1/1:118,41:100:99:2839,226,0 17 41244986 . A C 681.73 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-5.969;DP=161;Dels=0.01;FS=2.931;HRun=0;HaplotypeScore=102.8191;MQ=31.43;MQ0=0;MQRankSum=1.321;QD=4.23;ReadPosRankSum=-5.914 GT:AD:DP:GQ:PL 0/1:115,43:159:99:712,0,1648 17 41244986 . A AGC 5157.60 PASS AC=2;AF=1.00;AN=2;DP=160;FS=0.000;HRun=0;HaplotypeScore=434.0898;MQ=31.33;MQ0=0;QD=32.23 GT:AD:DP:GQ:PL 1/1:53,107:98:99:5158,280,0 17 41245023 rs28897684 T C 2837.29 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=0.515;DB;DP=152;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=10.6619;MQ=31.37;MQ0=0;MQRankSum=0.679;QD=18.67;ReadPosRankSum=1.709 GT:AD:DP:GQ:PL 1/1:4,148:152:99:2870,268,0 17 41245151 . AT A 407.69 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.767;DP=136;FS=1.696;HRun=3;HaplotypeScore=461.3082;MQ=30.28;MQ0=0;MQRankSum=-0.548;QD=3.00;ReadPosRankSum=3.173 GT:AD:DP:GQ:PL 1/1:105,28:75:65.96:450,66,0 17 41245154 rs80357850 TG T 2648.29 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-1.637;DB;DP=138;FS=0.000;HRun=2;HaplotypeScore=253.1819;MQ=30.44;MQ0=0;MQRankSum=0.925;QD=19.19;ReadPosRankSum=1.400 GT:AD:DP:GQ:PL 1/1:89,48:77:99:2690,211,0 17 41245156 . G T 1151.05 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=3.686;DP=136;Dels=0.00;FS=3.291;HRun=2;HaplotypeScore=72.5479;MQ=30.26;MQ0=0;MQRankSum=4.097;QD=8.46;ReadPosRankSum=1.607 GT:AD:DP:GQ:PL 0/1:84,52:136:99:1181,0,675 17 41245156 rs80357546 GT G 475.03 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.933;DB;DP=139;FS=2.078;HRun=2;HaplotypeScore=455.7325;MQ=30.41;MQ0=0;MQRankSum=-1.708;QD=3.42;ReadPosRankSum=3.055 GT:AD:DP:GQ:PL 1/1:89,50:77:56.49:517,56,0 17 41245420 . T TA 1401.09 PASS AC=2;AF=1.00;AN=2;DP=139;FS=0.000;HRun=4;HaplotypeScore=550.8821;MQ=33.95;MQ0=0;QD=10.08 GT:AD:DP:GQ:PL 1/1:96,41:80:99:1443,208,0 17 41245422 . A T 1112.03 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-1.757;DP=140;Dels=0.01;FS=4.345;HRun=0;HaplotypeScore=86.9620;MQ=34.01;MQ0=0;MQRankSum=4.770;QD=7.94;ReadPosRankSum=3.554 GT:AD:DP:GQ:PL 0/1:92,46:138:99:1142,0,841 17 41245423 . A T 637.74 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-2.469;DP=140;Dels=0.01;FS=2.069;HRun=0;HaplotypeScore=84.4224;MQ=33.97;MQ0=0;MQRankSum=4.337;QD=4.56;ReadPosRankSum=-5.857 GT:AD:DP:GQ:PL 0/1:107,32:139:99:668,0,1278 17 41245423 . A AA 1400.90 PASS AC=2;AF=1.00;AN=2;DP=141;FS=0.000;HRun=2;HaplotypeScore=575.0667;MQ=34.27;MQ0=0;QD=9.94 GT:AD:DP:GQ:PL 1/1:116,25:82:99:1443,207,0 17 41245476 rs80357688 CT C 3791.42 PASS AC=2;AF=1.00;AN=2;DB;DP=154;FS=0.000;HRun=4;HaplotypeScore=483.0603;MQ=37.55;MQ0=0;QD=24.62 GT:AD:DP:GQ:PL 1/1:13,141:109:99:3791,319,0 17 41245900 rs56012641 T G 4098.03 PASS AC=2;AF=1.00;AN=2;DB;DP=136;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=7.6738;MQ=41.34;MQ0=0;QD=30.13 GT:AD:DP:GQ:PL 1/1:1,134:136:99:4097,379,0 17 41248607 . A C 1100.23 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-2.822;DP=139;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=54.2640;MQ=25.68;MQ0=0;MQRankSum=3.335;QD=7.92;ReadPosRankSum=4.418 GT:AD:DP:GQ:PL 0/1:83,55:139:99:1130,0,780 17 41252697 rs10445302 T A 15.26 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=7.165;DB;DP=121;Dels=0.02;HRun=2;HaplotypeScore=14.0202;MQ=7.31;MQ0=0;MQRankSum=2.890;QD=0.13;ReadPosRankSum=6.240 GT:AD:DP:GQ:PL 1/1:35,83:118:5.98:46,6,0 17 41258531 rs80357084 G A 4495.52 PASS AC=2;AF=1.00;AN=2;DB;DP=149;Dels=0.01;FS=0.000;HRun=2;HaplotypeScore=13.6203;MQ=45.61;MQ0=0;QD=30.17 GT:AD:DP:GQ:PL 1/1:4,142:147:99:4495,391,0 17 41258946 rs799913 T C 3493.68 PASS AC=2;AF=1.00;AN=2;DB;DP=132;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.5018;MQ=40.62;MQ0=0;QD=26.47 GT:AD:DP:GQ:PL 1/1:0,132:132:99:3492,328,0 17 41266091 rs35757194 C CA 1656.67 PASS AC=2;AF=1.00;AN=2;DB;DP=163;FS=0.000;HRun=13;HaplotypeScore=134.6990;MQ=17.05;MQ0=0;QD=10.16 GT:AD:DP:GQ:PL 1/1:36,127:63:99:1699,183,0 17 41266407 rs77558167 C T 4322.98 PASS AC=2;AF=1.00;AN=2;DB;DP=161;Dels=0.02;FS=0.000;HRun=16;HaplotypeScore=17.9780;MQ=35.37;MQ0=0;QD=26.85 GT:AD:DP:GQ:PL 1/1:4,152:157:99:4321,409,0 17 41267747 rs80357327 A T 4375.31 PASS AC=2;AF=1.00;AN=2;DB;DP=147;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=14.2750;MQ=41.73;MQ0=0;QD=29.76 GT:AD:DP:GQ:PL 1/1:3,144:147:99:4374,394,0 17 41275391 rs12941042 T G 1213.06 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-0.691;DB;DP=141;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=6.5767;MQ=17.75;MQ0=0;MQRankSum=1.068;QD=8.60;ReadPosRankSum=2.414 GT:AD:DP:GQ:PL 1/1:4,136:141:99:1246,123,0 17 41276030 rs80358003 T A 217.37 PASS AC=2;AF=1.00;AN=2;DB;DP=112;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=8.0532;MQ=12.17;MQ0=0;QD=1.94 GT:AD:DP:GQ:PL 1/1:4,107:112:32.85:250,33,0 17 41276085 rs80359887 TCTTCAACGC T 1132.62 PASS AC=2;AF=1.00;AN=2;DB;DP=106;FS=0.000;HRun=0;HaplotypeScore=136.6791;MQ=12.78;MQ0=0;QD=10.69 GT:AD:DP:GQ:PL 1/1:5,99:12:36.12:1175,36,0 17 80411207 rs9896620 C G 5.06 LowQual AC=1;AF=0.50;AN=2;DB;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0000;MQ=45.00;MQ0=0;QD=5.06 GT:AD:DP:GQ:PL 0/1:0,1:1:1.76:33,3,0 17 80411212 . C A 6.39 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=45.00;MQ0=0;QD=6.39 GT:AD:DP:GQ:PL 0/1:0,1:1:1.76:35,3,0 17 80411215 . T A 5.06 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=45.00;MQ0=0;QD=5.06 GT:AD:DP:GQ:PL 0/1:0,1:1:1.76:33,3,0