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Created 2015-08-18 11:55:19 | Updated 2015-08-18 11:57:08 | Tags: unifiedgenotyper vcf lowqual emit-all-confident-sites emit-all-sites
Comments (14)

Hi,

I've run UnifiedGenotyper on a BAM file with both EMIT_ALL_SITES and EMIT_ALL_CONFIDENT_SITES. I've noticed some of the calls that have been omitted with the EMIT_ALL_SITES option seem to be of comparable quality to others that have been emitted. For example, sites like HE670865 368605 are removed as non-confident sites while the site 368591 has not been.

I understand why the positions flagged as "LowQual" are not present when using EMIT_ALL_CONFIDENT_SITES. But I can't see why other positions (such as HE670865 368605 and HE670865 368600) are not being emitted. Of particular importance is the fact that some of these seemingly 'good sites' that have been removed are SNPs that might be of biological importance.

These are the two commands used together with some relevant lines from the resulting vcfs:

java -Xmx4g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -nt 4 -out_mode EMIT_ALL_SITES -baq CALCULATE_AS_NECESSARY -hets 0.015 -R genome_ref.fasta -o output_all.vcf -I input_divergentscaffs.realign.bam &> divergentscaffs_out.GATKlog &

java -Xmx4g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -nt 4 -out_mode EMIT_ALL_CONFIDENT_SITES -baq CALCULATE_AS_NECESSARY -hets 0.015 -R genome_ref.fasta -o output_confident.vcf -I input_divergentscaffs.realign.bam &> divergentscaffs_confident.GATKlog &

These are a sample of lines from the outputted VCF file when using EMIT_ALL_SITES:

HE670865 368589 . A . 46.89 . AN=16;DP=441;MQ=43.26;MQ0=13 GT:DP 0/0:35 0/0:45 0/0:58 0/0:38 0/0:75 0/0:64 0/0:64 0/0:47 HE670865 368590 . A . 50.15 . AN=16;DP=447;MQ=43.41;MQ0=13 GT:DP 0/0:35 0/0:45 0/0:60 0/0:39 0/0:76 0/0:66 0/0:65 0/0:47 HE670865 368591 . A . 39.12 . AN=16;DP=448;MQ=43.32;MQ0=12 GT:DP 0/0:36 0/0:45 0/0:61 0/0:39 0/0:77 0/0:66 0/0:66 0/0:46 HE670865 368592 . C T 5437.28 . AC=16;AF=1.00;AN=16;BaseQRankSum=1.036;DP=445;Dels=0.06;FS=0.000;HaplotypeScore=99.1839;MLEAC=16;MLEAF=1.00;MQ=43.48;MQ0=9;MQRankSum=4.214;QD=12.22;ReadPosRankSum=6.263 GT:AD:DP:GQ:PL 1/1:1,27:29:27:296,27,0 1/1:0,45:45:30:344,30,0 1/1:6,43:52:33:327,33,0 1/1:1,38:39:48:506,48,0 1/1:5,68:76:99:1100,102,0 1/1:4,61:65:68:1068,68,0 1/1:0,65:66:99:1035,99,0 1/1:0,46:46:69:774,69,0 HE670865 368593 . A . 50.76 . AN=16;DP=448;MQ=43.48;MQ0=9 GT:DP 0/0:29 0/0:45 0/0:53 0/0:41 0/0:76 0/0:65 0/0:66 0/0:47 HE670865 368594 . G . 69.75 . AN=16;DP=449;MQ=43.48;MQ0=9 GT:DP 0/0:28 0/0:46 0/0:51 0/0:41 0/0:76 0/0:66 0/0:66 0/0:47 HE670865 368595 . A . 66.75 . AN=16;DP=447;MQ=43.43;MQ0=9 GT:DP 0/0:30 0/0:46 0/0:50 0/0:41 0/0:75 0/0:66 0/0:66 0/0:47 HE670865 368596 . A . 72.75 . AN=16;DP=445;MQ=43.54;MQ0=9 GT:DP 0/0:31 0/0:46 0/0:48 0/0:41 0/0:76 0/0:66 0/0:67 0/0:47 HE670865 368597 . G . 66.75 . AN=16;DP=442;MQ=43.48;MQ0=9 GT:DP 0/0:25 0/0:46 0/0:41 0/0:40 0/0:74 0/0:67 0/0:67 0/0:47 HE670865 368598 . A . 75.75 . AN=16;DP=444;MQ=43.44;MQ0=9 GT:DP 0/0:25 0/0:46 0/0:41 0/0:39 0/0:75 0/0:69 0/0:67 0/0:47 HE670865 368599 . A . 72.75 . AN=16;DP=445;MQ=43.49;MQ0=9 GT:DP 0/0:24 0/0:45 0/0:39 0/0:39 0/0:76 0/0:69 0/0:68 0/0:48 HE670865 368600 . T A 4405.18 . AC=8;AF=0.500;AN=16;BaseQRankSum=2.278;DP=441;Dels=0.08;FS=6.510;HaplotypeScore=100.3222;MLEAC=8;MLEAF=0.500;MQ=43.26;MQ0=9;MQRankSum=0.498;QD=24.75;ReadPosRankSum=1.103 GT:AD:DP:GQ:PL 1/1:3,19:22:48:570,48,0 1/1:2,45:47:99:1386,114,0 1/1:4,33:37:96:1196,96,0 1/1:0,38:38:99:1307,105,0 0/0:76,2:78:99:0,178,2196 0/0:65,0:65:99:0,159,2002 0/0:70,0:70:99:0,168,2042 0/0:49,0:49:99:0,129,1549 HE670865 368601 . T . 63.75 . AN=16;DP=442;MQ=43.37;MQ0=9 GT:DP 0/0:19 0/0:47 0/0:37 0/0:38 0/0:77 0/0:66 0/0:72 0/0:48 HE670865 368602 . A . 66.75 . AN=16;DP=444;MQ=43.44;MQ0=9 GT:DP 0/0:19 0/0:47 0/0:38 0/0:38 0/0:78 0/0:65 0/0:74 0/0:48 HE670865 368603 . C . 66.75 . AN=16;DP=441;MQ=43.50;MQ0=11 GT:DP 0/0:20 0/0:47 0/0:39 0/0:37 0/0:76 0/0:64 0/0:73 0/0:48 HE670865 368604 . A . 63.75 . AN=16;DP=441;MQ=43.24;MQ0=11 GT:DP 0/0:21 0/0:47 0/0:39 0/0:38 0/0:74 0/0:64 0/0:74 0/0:48 HE670865 368605 . G . 60.75 . AN=16;DP=436;MQ=43.17;MQ0=12 GT:DP 0/0:20 0/0:47 0/0:40 0/0:38 0/0:73 0/0:63 0/0:73 0/0:47 HE670865 368606 . A . 60.75 . AN=16;DP=436;MQ=43.05;MQ0=12 GT:DP 0/0:22 0/0:45 0/0:40 0/0:39 0/0:73 0/0:63 0/0:75 0/0:46 HE670865 368607 . T C 3984.32 . AC=15;AF=0.938;AN=16;BaseQRankSum=0.225;DP=433;Dels=0.06;FS=11.987;HaplotypeScore=229.2107;MLEAC=15;MLEAF=0.938;MQ=42.94;MQ0=12;MQRankSum=1.624;QD=9.20;ReadPosRankSum=-0.463 GT:AD:DP:GQ:PL 1/1:7,18:26:12:109,12,0 1/1:2,39:44:57:475,57,0 1/1:6,36:44:51:426,51,0 1/1:1,36:39:39:328,39,0 1/1:6,67:73:44:603,44,0 1/1:0,63:63:99:1016,105,0 1/1:4,69:74:90:817,90,0 0/1:22,23:46:99:232,0,373 HE670865 368608 . A . 24.45 LowQual AN=16;DP=438;MQ=42.86;MQ0=12 GT:DP 0/0:34 0/0:45 0/0:55 0/0:39 0/0:74 0/0:63 0/0:74 0/0:47 HE670865 368609 . A . 29.97 LowQual AN=14;DP=434;MQ=42.67;MQ0=12 GT:DP ./. 0/0:44 0/0:53 0/0:39 0/0:67 0/0:61 0/0:74 0/0:47 HE670865 368610 . A . 20.62 LowQual AN=16;DP=432;MQ=42.47;MQ0=12 GT:DP 0/0:33 0/0:45 0/0:54 0/0:39 0/0:67 0/0:59 0/0:71 0/0:47 HE670865 368611 . C A 434.85 . AC=13;AF=0.813;AN=16;BaseQRankSum=0.922;DP=420;Dels=0.17;FS=0.883;HaplotypeScore=330.1362;MLEAC=14;MLEAF=0.875;MQ=42.34;MQ0=12;MQRankSum=0.871;QD=1.13;ReadPosRankSum=-2.717 GT:AD:DP:GQ:PL 0/0:17,11:28:3:0,3,23 1/1:27,10:38:3:32,3,0 1/1:23,23:46:6:64,6,0 1/1:12,16:29:3:32,3,0 1/1:22,30:53:9:73,9,0 1/1:18,35:53:6:56,6,0 1/1:26,34:60:18:188,18,0 0/1:23,17:40:16:16,0,61 HE670865 368612 . A . 6.62 LowQual AN=16;DP=409;MQ=42.14;MQ0=12 GT:DP 0/0:27 0/0:35 0/0:36 0/0:26 0/0:49 0/0:47 0/0:55 0/0:31 HE670865 368613 . G A 325 . AC=11;AF=0.917;AN=12;BaseQRankSum=3.200;DP=404;Dels=0.46;FS=1.094;HaplotypeScore=347.5139;MLEAC=11;MLEAF=0.917;MQ=41.95;MQ0=12;MQRankSum=1.300;QD=1.02;ReadPosRankSum=1.782 GT:AD:DP:GQ:PL 1/1:4,16:21:3:22,3,0 ./. 1/1:0,25:26:3:23,3,0 1/1:1,15:21:3:26,3,0 0/1:4,28:36:10:62,0,10 1/1:1,35:36:6:52,6,0 1/1:2,35:39:15:156,15,0 ./. HE670865 368614 . A . 17.30 LowQual AN=12;DP=416;MQ=41.75;MQ0=12 GT:DP ./. 0/0:25 0/0:36 ./. 0/0:47 0/0:41 0/0:50 0/0:25 HE670865 368615 . A . 16.42 LowQual AN=12;DP=411;MQ=41.66;MQ0=11 GT:DP ./. 0/0:25 0/0:35 ./. 0/0:45 0/0:40 0/0:49 0/0:22 HE670865 368616 . A . 17.42 LowQual AN=10;DP=406;MQ=41.71;MQ0=10 GT:DP ./. 0/0:24 ./. ./. 0/0:40 0/0:40 0/0:47 0/0:22 HE670865 368617 . T C 94.41 . AC=4;AF=0.667;AN=6;BaseQRankSum=0.262;DP=385;Dels=0.38;FS=7.489;HaplotypeScore=362.4384;MLEAC=5;MLEAF=0.833;MQ=41.72;MQ0=9;MQRankSum=1.775;QD=0.84;ReadPosRankSum=4.850 GT:AD:DP:GQ:PL ./. 0/0:15,1:20:3:0,3,32 ./. ./. ./. 1/1:5,31:36:9:85,9,0 1/1:14,28:42:3:26,3,0 ./. HE670865 368618 . C . 17.27 LowQual AN=6;DP=370;MQ=41.65;MQ0=8 GT:DP ./. 0/0:10 ./. ./. ./. 0/0:34 0/0:37 ./. HE670865 368619 . G A 35.14 . AC=4;AF=0.500;AN=8;BaseQRankSum=-3.320;DP=365;Dels=0.54;FS=0.000;HaplotypeScore=399.7009;MLEAC=4;MLEAF=0.500;MQ=41.71;MQ0=8;MQRankSum=-1.237;QD=0.35;ReadPosRankSum=-4.879 GT:AD:DP:GQ:PL ./. 1/1:0,4:8:3:28,3,0 ./. ./. 0/0:17,3:22:3:0,3,23 0/0:31,3:34:3:0,3,22 1/1:28,8:36:3:25,3,0 ./. HE670865 368620 . T . 15.82 LowQual AN=2;DP=358;MQ=41.72;MQ0=8 GT:DP ./. 0/0:8 ./. ./. ./. ./. ./. ./. HE670865 368621 . T . . . DP=358;MQ=41.63;MQ0=8 GT ./. ./. ./. ./. ./. ./. ./. ./. HE670865 368622 . T . 14.11 LowQual AN=6;DP=358;MQ=41.53;MQ0=8 GT:DP ./. ./. ./. ./. ./. 0/0:11 0/0:19 0/0:17 HE670865 368623 . T . 14.11 LowQual AN=6;DP=365;MQ=41.46;MQ0=7 GT:DP ./. 0/0:24 ./. 0/0:16 ./. 0/0:20 ./. ./. HE670865 368624 . A . 13.85 LowQual AN=8;DP=366;MQ=41.48;MQ0=7 GT:DP 0/0:22 0/0:26 ./. 0/0:23 ./. 0/0:20 ./. ./. HE670865 368625 . T . 14.12 LowQual AN=6;DP=353;MQ=41.39;MQ0=7 GT:DP 0/0:20 0/0:26 ./. ./. ./. 0/0:18 ./. ./. HE670865 368626 . T . . . DP=348;MQ=41.31;MQ0=7 GT ./. ./. ./. ./. ./. ./. ./. ./. HE670865 368627 . T A 15.18 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=-1.221;DP=348;Dels=0.55;FS=0.000;HaplotypeScore=403.2395;MLEAC=2;MLEAF=1.00;MQ=41.29;MQ0=7;MQRankSum=-0.971;QD=0.23;ReadPosRankSum=-0.344 GT:AD:DP:GQ:PL ./. ./. ./. ./. 1/1:30,4:34:3:26,3,0 ./. ./. ./. HE670865 368628 . T . 13.85 LowQual AN=8;DP=357;MQ=41.07;MQ0=8 GT:DP ./. 0/0:22 ./. 0/0:10 0/0:33 0/0:15 ./. ./. HE670865 368629 . A . 15.14 LowQual AN=10;DP=357;MQ=40.99;MQ0=8 GT:DP 0/0:14 0/0:22 ./. ./. 0/0:34 0/0:15 0/0:21 ./. HE670865 368630 . T . 18.75 LowQual AN=10;DP=358;MQ=40.89;MQ0=8 GT:DP 0/0:15 0/0:23 ./. 0/0:12 ./. 0/0:16 0/0:21 ./. HE670865 368631 . C . 18.33 LowQual AN=14;DP=359;MQ=40.70;MQ0=8 GT:DP 0/0:15 0/0:23 0/0:14 ./. 0/0:30 0/0:16 0/0:20 0/0:33 HE670865 368632 . G . 17.87 LowQual AN=16;DP=361;MQ=40.63;MQ0=9 GT:DP 0/0:15 0/0:23 0/0:15 0/0:12 0/0:29 0/0:16 0/0:21 0/0:33 HE670865 368633 . T . 18.90 LowQual AN=14;DP=364;MQ=40.51;MQ0=10 GT:DP 0/0:17 0/0:24 0/0:16 ./. 0/0:32 0/0:17 0/0:22 0/0:34 HE670865 368634 . A . 17 LowQual AN=14;DP=369;MQ=40.67;MQ0=10 GT:DP 0/0:18 0/0:24 0/0:18 ./. 0/0:36 0/0:19 0/0:22 0/0:34 HE670865 368635 . T . 17.22 LowQual AN=14;DP=364;MQ=40.66;MQ0=10 GT:DP 0/0:18 0/0:24 0/0:22 ./. 0/0:37 0/0:20 0/0:21 0/0:32 HE670865 368636 . C . 16.03 LowQual AN=14;DP=362;MQ=40.70;MQ0=10 GT:DP 0/0:16 ./. 0/0:15 0/0:14 0/0:36 0/0:20 0/0:22 0/0:29 HE670865 368637 . A . 0.02 LowQual AN=8;DP=356;MQ=40.91;MQ0=11 GT:DP 0/0:26 ./. 0/0:49 0/0:31 0/0:55 ./. ./. ./. HE670865 368638 . T G 24.10 LowQual AC=3;AF=0.250;AN=12;BaseQRankSum=-6.075;DP=355;Dels=0.14;FS=8.612;HaplotypeScore=349.9679;MLEAC=3;MLEAF=0.250;MQ=40.80;MQ0=12;MQRankSum=-2.113;QD=0.24;ReadPosRankSum=1.216 GT:AD:DP:GQ:PL ./. 0/0:22,3:25:6:0,6,44 0/0:46,3:49:6:0,6,44 0/0:29,1:30:6:0,6,49 0/0:46,8:54:3:0,3,22 1/1:40,2:42:3:29,3,0 0/1:47,5:52:17:18,0,17 ./. HE670865 368639 . A . 18.78 LowQual AN=16;DP=352;MQ=40.91;MQ0=13 GT:DP 0/0:25 0/0:26 0/0:48 0/0:30 0/0:52 0/0:42 0/0:50 0/0:26 HE670865 368640 . T . 20.94 LowQual AN=16;DP=351;MQ=40.93;MQ0=13 GT:DP 0/0:25 0/0:26 0/0:48 0/0:30 0/0:51 0/0:42 0/0:50 0/0:26 HE670865 368641 . C . 23.55 LowQual AN=16;DP=347;MQ=40.91;MQ0=13 GT:DP 0/0:24 0/0:25 0/0:49 0/0:26 0/0:45 0/0:39 0/0:47 0/0:18 HE670865 368642 . G T 24 LowQual AC=4;AF=0.250;AN=16;BaseQRankSum=-1.989;DP=349;Dels=0.21;FS=7.313;HaplotypeScore=259.1726;MLEAC=3;MLEAF=0.188;MQ=40.80;MQ0=13;MQRankSum=-2.006;QD=0.14;ReadPosRankSum=1.275 GT:AD:DP:GQ:PL 0/1:21,3:24:11:11,0,88 0/0:23,3:26:18:0,18,152 0/0:47,2:49:30:0,30,252 0/0:25,0:25:30:0,30,256 0/0:38,7:45:18:0,18,164 0/1:37,2:39:27:27,0,177 0/1:43,4:47:2:2,0,144 0/1:13,6:19:13:13,0,79 HE670865 368643 . T . 27.64 LowQual AN=16;DP=345;MQ=40.82;MQ0=13 GT:DP 0/0:24 0/0:26 0/0:49 0/0:26 0/0:44 0/0:38 0/0:46 0/0:20 HE670865 368644 . A . 26.97 LowQual AN=14;DP=343;MQ=40.74;MQ0=13 GT:DP ./. 0/0:22 0/0:47 0/0:26 0/0:36 0/0:37 0/0:42 0/0:17 HE670865 368645 . T . 20.86 LowQual AN=14;DP=340;MQ=40.85;MQ0=12 GT:DP ./. 0/0:21 0/0:47 0/0:26 0/0:36 0/0:36 0/0:41 0/0:17 HE670865 368646 . G C,T 237.20 . AC=5,7;AF=0.417,0.583;AN=12;BaseQRankSum=-1.775;DP=353;Dels=0.25;FS=0.000;HaplotypeScore=196.6140;MLEAC=5,6;MLEAF=0.417,0.500;MQ=40.93;MQ0=12;MQRankSum=-0.594;QD=0.89;ReadPosRankSum=1.392 GT:AD:DP:GQ:PL ./. 2/2:13,14,7:34:3:30,30,30,3,3,0 ./. 1/2:2,13,5:20:15:80,24,15,56,0,53 1/2:10,27,9:46:14:64,20,14,44,0,41 1/2:4,32,2:38:18:61,24,18,37,0,34 2/2:8,30,8:46:9:77,77,77,9,9,0 1/1:18,11,1:30:6:43,6,0,43,6,43 HE670865 368647 . T . 29.30 LowQual AN=16;DP=368;MQ=40.74;MQ0=12 GT:DP 0/0:31 0/0:37 0/0:54 0/0:36 0/0:52 0/0:42 0/0:50 0/0:34 HE670865 368648 . G . 51.60 . AN=16;DP=366;MQ=40.87;MQ0=12 GT:DP 0/0:34 0/0:40 0/0:57 0/0:37 0/0:59 0/0:44 0/0:53 0/0:42

These are the comparable lines from the outputted VCF when using EMIT_ALL_CONFIDENT_SITES:

HE670865 368589 . A . 46.89 . AN=16;DP=441;MQ=43.26;MQ0=13 GT:DP 0/0:35 0/0:45 0/0:58 0/0:38 0/0:75 0/0:64 0/0:64 0/0:47 HE670865 368590 . A . 50.15 . AN=16;DP=447;MQ=43.41;MQ0=13 GT:DP 0/0:35 0/0:45 0/0:60 0/0:39 0/0:76 0/0:66 0/0:65 0/0:47 HE670865 368591 . A . 39.12 . AN=16;DP=448;MQ=43.32;MQ0=12 GT:DP 0/0:36 0/0:45 0/0:61 0/0:39 0/0:77 0/0:66 0/0:66 0/0:46 HE670865 368648 . G . 51.60 . AN=16;DP=366;MQ=40.87;MQ0=12 GT:DP 0/0:34 0/0:40 0/0:57 0/0:37 0/0:59 0/0:44 0/0:53 0/0:42 HE670865 368649 . T . 75.72 . AN=16;DP=368;MQ=40.89;MQ0=12 GT:DP 0/0:34 0/0:41 0/0:57 0/0:38 0/0:59 0/0:44 0/0:53 0/0:42 HE670865 368650 . T . 72.74 . AN=16;DP=369;MQ=40.87;MQ0=12 GT:DP 0/0:34 0/0:41 0/0:57 0/0:38 0/0:59 0/0:44 0/0:53 0/0:43 HE670865 368651 . T . 87.71 . AN=16;DP=369;MQ=40.88;MQ0=12 GT:DP 0/0:33 0/0:42 0/0:58 0/0:37 0/0:59 0/0:44 0/0:53 0/0:43 HE670865 368652 . T . 93.72 . AN=16;DP=373;MQ=40.89;MQ0=12 GT:DP 0/0:32 0/0:43 0/0:59 0/0:37 0/0:59 0/0:45 0/0:54 0/0:43

Any help or insight would be greatly appreciated.


Created 2013-05-14 10:04:51 | Updated | Tags: combinevariants filter pass lowqual
Comments (5)

When using CombineVariants, my variants get a FILTER value of either PASS or LowQual. Would it be possible to add an option to CombineVariants which prevents the FILTER value to be set to PASS? Otherwise I have to do some file processing before I run ApplyRecalibration further downstream. It would be great if this was a feature of all walkers and not just VariantFiltration. I'm not sure if the forum is the right place for feature requests. Happy to use Bugzilla or similar instead. Thanks.