##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_29.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 15365659 . G A 5.06 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=34.00;MQ0=0;QD=5.06 GT:AD:DP:GQ:PL 0/1:0,1:1:1.76:33,3,0 17 19855092 . T C 5.06 LowQual AC=1;AF=0.50;AN=2;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 19855113 . G T 5.72 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=45.00;MQ0=0;QD=5.72 GT:AD:DP:GQ:PL 0/1:0,1:1:1.76:34,3,0 17 19855119 . A T 5.72 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0000;MQ=45.00;MQ0=0;QD=5.72 GT:AD:DP:GQ:PL 0/1:0,1:1:1.76:34,3,0 17 41196309 . T G 5.06 LowQual AC=1;AF=0.50;AN=2;DP=1;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=43.00;MQ0=0;QD=5.06 GT:AD:DP:GQ:PL 0/1:0,1:1:1.76:33,3,0 17 41196309 . T TGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6824.44 PASS AC=2;AF=1.00;AN=2;DP=42;FS=0.000;HRun=2;HaplotypeScore=590.9086;MQ=30.45;MQ0=0;QD=162.49 GT:AD:DP:GQ:PL 1/1:2,2:30:87.29:6824,87,0 17 41200109 rs4793190 T C 2013.07 PASS AC=2;AF=1.00;AN=2;DB;DP=159;Dels=0.01;FS=0.000;HRun=2;HaplotypeScore=17.7381;MQ=20.19;MQ0=0;QD=12.66 GT:AD:DP:GQ:PL 1/1:5,151:157:99:2046,210,0 17 41203065 rs80358148 C G 2470.49 PASS AC=2;AF=1.00;AN=2;DB;DP=145;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.3302;MQ=34.40;MQ0=0;QD=17.04 GT:AD:DP:GQ:PL 1/1:3,142:145:99:2503,235,0 17 41203090 rs80357818 G GT 807.38 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=3.323;DB;DP=150;FS=5.155;HRun=2;HaplotypeScore=618.4161;MQ=33.14;MQ0=0;MQRankSum=-0.065;QD=5.38;ReadPosRankSum=2.984 GT:AD:DP:GQ:PL 1/1:127,19:76:86.85:849,87,0 17 41203092 . T G 406.43 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-3.929;DP=153;Dels=0.00;FS=2.097;HRun=2;HaplotypeScore=81.2811;MQ=33.84;MQ0=0;MQRankSum=3.649;QD=2.66;ReadPosRankSum=-5.079 GT:AD:DP:GQ:PL 0/1:126,26:153:99:436,0,1507 17 41203092 . T TG 2853.22 PASS AC=2;AF=1.00;AN=2;DP=152;FS=0.000;HRun=2;HaplotypeScore=450.2767;MQ=33.76;MQ0=0;QD=18.77 GT:AD:DP:GQ:PL 1/1:36,116:78:99:2895,208,0 17 41203115 rs80357463 A C 2265.64 PASS AC=2;AF=1.00;AN=2;DB;DP=147;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=3.9038;MQ=39.49;MQ0=0;QD=15.41 GT:AD:DP:GQ:PL 1/1:1,145:146:99:2299,208,0 17 41207462 rs62076408 C A 2038.67 PASS AC=2;AF=1.00;AN=2;DB;DP=144;Dels=0.02;FS=0.000;HRun=2;HaplotypeScore=8.8150;MQ=17.59;MQ0=0;QD=14.16 GT:AD:DP:GQ:PL 1/1:1,139:141:99:2072,243,0 17 41213506 rs79826053 C A 2700.61 PASS AC=2;AF=1.00;AN=2;DB;DP=133;Dels=0.01;FS=0.000;HRun=2;HaplotypeScore=3.4975;MQ=42.23;MQ0=0;QD=20.31 GT:AD:DP:GQ:PL 1/1:1,131:132:99:2734,241,0 17 41215899 rs45444999 C T 3505.97 PASS AC=2;AF=1.00;AN=2;DB;DP=131;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=7.3800;MQ=48.53;MQ0=0;QD=26.76 GT:AD:DP:GQ:PL 1/1:0,130:130:99:3505,310,0 17 41215950 rs80357710 TCA T 2111.07 PASS AC=2;AF=1.00;AN=2;DB;DP=116;FS=0.000;HRun=0;HaplotypeScore=398.5256;MQ=39.44;MQ0=0;QD=18.20 GT:AD:DP:GQ:PL 1/1:35,79:67:99:2153,163,0 17 41215957 rs80357125 C A 520.21 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=4.985;DB;DP=111;Dels=0.02;FS=26.917;HRun=3;HaplotypeScore=89.9176;MQ=37.91;MQ0=0;MQRankSum=4.703;QD=4.69;ReadPosRankSum=-5.946 GT:AD:DP:GQ:PL 0/1:87,22:109:99:550,0,1002 17 41215957 rs80357760 CAA C 333.56 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=3.393;DB;DP=111;FS=1.639;HRun=3;HaplotypeScore=501.8965;MQ=37.91;MQ0=0;MQRankSum=0.221;QD=3.01;ReadPosRankSum=3.731 GT:AD:DP:GQ:PL 1/1:94,17:61:7.21:374,7,0 17 41219679 rs80358343 TGTG T 2357.45 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-1.732;DB;DP=140;FS=6.284;HRun=0;HaplotypeScore=298.1891;MQ=26.66;MQ0=0;MQRankSum=0.781;QD=16.84;ReadPosRankSum=0.102 GT:AD:DP:GQ:PL 1/1:29,110:56:99:2399,135,0 17 41219683 . G T 263.68 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=2.110;DP=135;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=135.8871;MQ=25.51;MQ0=0;MQRankSum=3.491;QD=1.95;ReadPosRankSum=-5.792 GT:AD:DP:GQ:PL 0/1:112,22:135:99:294,0,1046 17 41219683 . GTGT G 950.34 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-1.732;DP=136;FS=6.021;HRun=0;HaplotypeScore=413.3454;MQ=25.43;MQ0=0;MQRankSum=0.794;QD=6.99;ReadPosRankSum=-0.144 GT:AD:DP:GQ:PL 1/1:120,16:51:95.87:992,96,0 17 41220272 rs8176230 C T 1089.15 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.707;DB;DP=140;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=6.2415;MQ=16.78;MQ0=0;MQRankSum=1.431;QD=7.78;ReadPosRankSum=1.632 GT:AD:DP:GQ:PL 1/1:2,137:139:99:1122,111,0 17 41226734 rs8176211 ATGGGG A 1173.04 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=4.166;DB;DP=125;FS=3.820;HRun=0;HaplotypeScore=496.3999;MQ=24.81;MQ0=0;MQRankSum=-0.196;QD=9.38;ReadPosRankSum=3.719 GT:AD:DP:GQ:PL 0/1:112,13:52:32.50:1212,0,33 17 41226736 rs34250703 GGGGTT G 2582.70 PASS AC=2;AF=1.00;AN=2;DB;DP=123;FS=0.000;HRun=0;HaplotypeScore=358.2521;MQ=24.58;MQ0=0;QD=21.00 GT:AD:DP:GQ:PL 1/1:24,99:50:99:2625,132,0 17 41232344 rs6416927 G C 1911.87 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.676;DB;DP=125;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=6.5839;MQ=31.37;MQ0=0;MQRankSum=0.643;QD=15.29;ReadPosRankSum=1.173 GT:AD:DP:GQ:PL 1/1:1,123:125:99:1945,192,0 17 41244138 rs80357297 A G 3834.18 PASS AC=2;AF=1.00;AN=2;DB;DP=148;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=15.2379;MQ=41.00;MQ0=0;QD=25.91 GT:AD:DP:GQ:PL 1/1:2,145:147:99:3831,393,0 17 41244190 rs80357827 CA C 6200.71 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=-1.709;DB;DP=159;FS=3.430;HRun=2;HaplotypeScore=797.7782;MQ=42.02;MQ0=0;MQRankSum=-1.231;QD=39.00;ReadPosRankSum=1.709 GT:AD:DP:GQ:PL 1/1:6,153:154:99:6201,447,0 17 41244252 rs80357201 G A 5123.10 PASS AC=2;AF=1.00;AN=2;DB;DP=164;Dels=0.02;FS=0.000;HRun=1;HaplotypeScore=4.4038;MQ=41.70;MQ0=0;QD=31.24 GT:AD:DP:GQ:PL 1/1:0,160:161:99:5122,448,0 17 41244613 rs80357741 GA G 5229.42 PASS AC=2;AF=1.00;AN=2;DB;DP=133;FS=0.000;HRun=1;HaplotypeScore=676.5468;MQ=41.13;MQ0=0;QD=39.32 GT:AD:DP:GQ:PL 1/1:2,130:129:99:5229,382,0 17 41244627 rs80356872 A G 3667.59 PASS AC=2;AF=1.00;AN=2;DB;DP=124;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=9.2197;MQ=41.41;MQ0=0;QD=29.58 GT:AD:DP:GQ:PL 1/1:4,119:123:99:3667,337,0 17 41246038 rs80357445 G A 4411.17 PASS AC=2;AF=1.00;AN=2;DB;DP=135;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=8.4813;MQ=42.35;MQ0=0;QD=32.68 GT:AD:DP:GQ:PL 1/1:1,134:135:99:4410,397,0 17 41246420 rs80357821 AT A 3714.55 PASS AC=2;AF=1.00;AN=2;DB;DP=115;FS=0.000;HRun=3;HaplotypeScore=345.7389;MQ=41.81;MQ0=0;QD=32.30 GT:AD:DP:GQ:PL 1/1:10,104:108:99:3715,304,0 17 41251809 rs80357758 GA G 6067.38 PASS AC=2;AF=1.00;AN=2;DB;DP=159;FS=0.000;HRun=1;HaplotypeScore=493.5027;MQ=41.14;MQ0=0;QD=38.16 GT:AD:DP:GQ:PL 1/1:4,155:148:99:6067,442,0 17 41256266 rs28897673 T C 2903.12 PASS AC=2;AF=1.00;AN=2;DB;DP=114;Dels=0.01;FS=0.000;HRun=0;HaplotypeScore=10.4795;MQ=41.84;MQ0=0;QD=25.47 GT:AD:DP:GQ:PL 1/1:2,111:113:99:2936,277,0 17 41256904 rs80359879 CTGAAAAGCACAAA C 12342.11 PASS AC=2;AF=1.00;AN=2;DB;DP=113;FS=0.000;HRun=0;HaplotypeScore=1469.7649;MQ=48.90;MQ0=0;QD=109.22 GT:AD:DP:GQ:PL 1/1:18,95:112:99:12342,322,0 17 41256907 . A ATTTT 501.21 PASS AC=1;AF=0.50;AN=2;BaseQRankSum=-6.625;DP=109;FS=3.538;HRun=0;HaplotypeScore=2004.2668;MQ=48.30;MQ0=0;MQRankSum=0.212;QD=4.60;ReadPosRankSum=-6.242 GT:AD:DP:GQ:PL 0/1:98,1:108:99:540,0,1930 17 41258471 rs80358026 A G 4441.05 PASS AC=2;AF=1.00;AN=2;DB;DP=146;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=6.2271;MQ=44.95;MQ0=0;QD=30.42 GT:AD:DP:GQ:PL 1/1:4,140:146:99:4413,400,0 17 41260789 rs71361503 T TG 336.07 PASS AC=2;AF=1.00;AN=2;DB;DP=147;FS=0.000;HRun=3;HaplotypeScore=20.7142;MQ=11.67;MQ0=0;QD=2.29 GT:AD:DP:GQ:PL 1/1:69,77:9:27.09:378,27,0 17 41261343 rs117190188 G T 3567.72 PASS AC=2;AF=1.00;AN=2;DB;DP=125;Dels=0.02;FS=0.000;HRun=2;HaplotypeScore=13.7107;MQ=37.20;MQ0=0;QD=28.54 GT:AD:DP:GQ:PL 1/1:5,118:123:99:3567,316,0 17 41261563 rs8065872 A T 4054.89 PASS AC=2;AF=1.00;AN=2;DB;DP=132;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=9.4402;MQ=41.77;MQ0=0;QD=30.72 GT:AD:DP:GQ:PL 1/1:1,129:132:99:4027,358,0 17 41266352 rs79415432 G A 4444.54 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.710;DB;DP=158;Dels=0.01;FS=0.000;HRun=3;HaplotypeScore=13.1713;MQ=41.52;MQ0=0;MQRankSum=-0.270;QD=28.13;ReadPosRankSum=-0.022 GT:AD:DP:GQ:PL 1/1:4,153:157:99:4443,415,0 17 41277822 rs77018036 G T 3574.89 PASS AC=2;AF=1.00;AN=2;DB;DP=155;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=13.7130;MQ=27.65;MQ0=0;QD=23.06 GT:AD:DP:GQ:PL 1/1:1,154:155:99:3572,369,0 17 41278725 rs799907 C G 1710.47 PASS AC=2;AF=1.00;AN=2;DB;DP=131;Dels=0.02;FS=0.000;HRun=2;HaplotypeScore=6.2332;MQ=19.26;MQ0=0;QD=13.06 GT:AD:DP:GQ:PL 1/1:2,124:128:99:1743,180,0