Quantcast
Channel: haplotypecaller — GATK-Forum
Viewing all articles
Browse latest Browse all 1335

HaplotypeCaller seems not working well for several of my samples

$
0
0

Hi,

I am using the GATK v3.1-1-g07a4bf8. It seems to me that HaplotypeCaller made quite a lot more heterozygous calls for several of my samples. As you can see from the scatter plot, for those individuals (every dot means one individual) in the red parallelogram, HaplotypeCaller made on average 1500 heterozygote calls than UnifiedGenotyper. For other individuals, the number of heterozygous genotypes called by both callers are similar. One thing I should point out, those one in the red parallelogram did use a different capture array. But when I ran HaplotypeCaller and UnifiedGenotyper I did provide all bam files (joint genotyping all my 87 samples) and used the same interval file. I checked the raw VCF file, one line is attached here.

16 29818864 . C G 534.97 PASS AC=24;AF=0.145;AN=166;BaseQRankSum=-4.753;ClippingRankSum=-2.284;DP=1251;FS=0.000;InbreedingCoeff=-0.1260;MLEAC=21;MLEAF=0.127;MQ=59.97;MQ0=0;MQRankSum=-0.374;NEGATIVE_TRAIN_SITE;QD=2.03;ReadPosRankSum=-4.426;VQSLOD=-1.830e+00;culprit=MQ GT:AD:DP:GQ:PL 0/1:20,0:20:40:40,0,1402 0/0:19,0:19:60:0,60,1306 0/0:19,0:19:23:0,23,1295 0/1:14,0:14:23:23,0,986 0/1:5,0:5:19:19,0,336 0/1:7,0:7:7:7,0,510 0/0:5,0:5:15:0,15,324 0/1:8,1:9:49:49,0,493 0/1:32,1:33:17:17,0,2292 0/0:7,0:7:21:0,21,451 0/1:7,0:7:8:8,0,388 0/0:6,0:6:14:0,14,399 0/1:25,0:25:9:9,0,1722 0/0:4,0:4:12:0,12,279 0/0:23,0:23:36:0,36,1487 0/0:22,0:22:39:0,39,1532 0/0:9,0:9:27:0,27,534 0/0:23,0:23:46:0,46,1714 0/0:26,0:26:51:0,51,1780 0/1:26,0:26:16:16,0,1855 0/0:32,1:33:53:0,53,2150 0/0:33,0:33:17:0,17,2247 0/0:20,0:20:4:0,4,1446 0/0:1,0:1:6:0,6,62 0/0:3,0:3:9:0,9,236 0/0:33,0:33:99:0,105,2403 0/0:31,0:31:93:0,93,2189 0/0:39,0:39:85:0,85,2665 0/0:36,0:36:79:0,79,2536 0/0:16,0:16:48:0,48,1105 0/0:1,0:1:3:0,3,58 0/0:18,0:18:54:0,54,1325 0/0:22,0:22:37:0,37,1594 0/0:35,0:35:45:0,45,2273 0/1:26,0:26:1:1,0,1774 ./. 0/0:3,0:3:9:0,9,196 0/1:18,0:18:9:9,0,1298 0/0:1,0:1:6:0,6,106 0/0:15,0:15:45:0,45,1102 0/0:3,0:3:9:0,9,218 0/0:35,1:36:57:0,57,2510 ./. ./. 0/0:18,0:18:57:0,57,1353 0/0:16,0:16:22:0,22,1239 0/0:13,0:13:39:0,39,854 0/0:3,0:3:9:0,9,185 0/0:2,0:2:12:0,12,210 0/0:16,0:16:48:0,48,1123 0/0:21,0:21:52:0,52,1495 0/0:2,0:2:9:0,9,192 0/1:20,2:22:41:41,0,1384 0/0:5,0:5:15:0,15,360 0/0:16,0:16:14:0,14,1185 0/0:1,0:1:6:0,6,97 0/0:2,0:2:6:0,6,144 0/0:3,0:3:9:0,9,174 0/0:4,0:4:12:0,12,293 0/0:1,0:1:3:0,3,69 0/0:28,0:28:84:0,84,1988 0/0:29,0:29:96:0,96,2174 0/0:33,0:33:76:0,76,2174 ./. 0/0:3,0:3:9:0,9,225 0/0:20,0:20:29:0,29,1444 0/0:2,0:2:6:0,6,129 0/0:13,0:13:6:0,6,964 0/0:35,0:35:47:0,47,2432 0/0:25,1:26:62:0,62,1885 0/0:27,0:27:84:0,84,1806 0/0:31,0:31:79:0,79,2217 0/0:31,0:31:65:0,65,2182 0/0:34,0:34:99:0,114,2517 0/1:2,1:3:17:17,0,88 0/1:3,0:3:99:112,0,186 0/1:3,0:3:5:5,0,167 1/1:.:.:3:10,3,0 0/0:3,0:3:12:0,12,215 0/1:8,1:9:43:43,0,473 0/1:2,0:2:39:39,0,131 0/1:6,0:6:68:68,0,386 0/1:12,1:13:64:64,0,767 0/1:5,0:5:99:113,0,297 0/0:5,0:5:8:0,8,323 0/1:3,0:3:18:18,0,148 0/1:4,0:4:17:17,0,235

Looks like HaplotypeCaller incorrectly made some heterozygous calls for some individuals, especially when the read depth is not very high.

This is part of the log from the GATK.

INFO 11:06:37,484 HelpFormatter - -------------------------------------------------------------------------------- INFO 11:06:37,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-1-g07a4bf8, Compiled 2014/03/18 06:09:21 INFO 11:06:37,486 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:06:37,486 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 11:06:37,484 HelpFormatter - -------------------------------------------------------------------------------- INFO 11:06:37,487 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-1-g07a4bf8, Compiled 2014/03/18 06:09:21 INFO 11:06:37,487 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:06:37,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 11:06:37,490 HelpFormatter - Program Args: -T HaplotypeCaller -l INFO -R /data/houl3/Amish/Reference/human_g1k_v37_decoy.fasta -I sample1.bam -I sample2.bam -I sample3.bam -I ... -I sample87.bam --dbsnp /data/houl3/Amish/Reference/dbsnp_138.b37.vcf -o output.vcf --intervals Exome.bed -stand_call_conf 30.0 -stand_emit_conf 30.0


Viewing all articles
Browse latest Browse all 1335

Latest Images

Trending Articles



Latest Images