Hi GATK team,
I am working on a pipeline for exome sequencing variant calling. And I am only interested in the genotype for some specific positions so I used GENOTYPE_GIVEN_ALLELES mode with given vcf file. I only have "chromosome position ID REF ALT" info so I keeped other columns as . . I found that this mode is super slow, compared with discovery mode. And when it finished I found most of my records are marked with LowQual, but they have good sequencing depth and quality score. Can you tell me why they are marked with LowQual flag. Here are some output:
chr10 101421279 rs35229854 G A 0 LowQual AC=0;AF=0.00;AN=2;DB;DP=80;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=60.00;SOR=0.407 GT:AD:DP:GQ:PL 0/0:80,0:80:99:0,241,2781
chr10 101421288 rs147747082 C A 0 LowQual AC=0;AF=0.00;AN=2;DB;DP=81;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=60.00;SOR=0.332 GT:AD:DP:GQ:PL 0/0:81,0:81:99:0,244,2812
chr10 101421324 rs150267092 A G 0 LowQual AC=0;AF=0.00;AN=2;DB;DP=64;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=60.00;SOR=0.173 GT:AD:DP:GQ:PL 0/0:64,0:64:99:0,193,2224
chr10 101421366 rs370286436 C T 0 LowQual AC=0;AF=0.00;AN=2;DB;DP=59;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=60.00;SOR=0.101 GT:AD:DP:GQ:PL 0/0:59,0:59:99:0,178,2052
chr10 101421367 rs61729539 G A 0 LowQual AC=0;AF=0.00;AN=2;DB;DP=58;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=60.00;SOR=0.105 GT:AD:DP:GQ:PL 0/0:58,0:58:99:0,175,2014
chr10 101451259 rs11190245 T C 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;ClippingRankSum=2.143;DB;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.119;QD=18.93;ReadPosRankSum=1.904;SOR=0.507 GT:AD:DP:GQ:PL 0/1:11,21:32:99:634,0,286
I used default setting for other step. references are from gatk-bundle-2.8-hg19
Thanks for your help : )