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Hello, Here is part of a vcf generated by GATK Unified Genotyper :
chr4 106196323 . TCAGA T 32729.73 LowQD AC=1;AF=0.500;AN=2;BaseQRankSum=21.836;DP=6712;FS=8.862;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=9.297;QD=1.22;RPA=2,1;RU=CAGA;ReadPosRankSum=7.319;STR GT:AD:DP:GQ:PL 0/1:4452,1723:6710:99:32767,0,32767
chr4 106196951 rs2454206 A G 5061.77 PASS ABHet=0.497;AC=1;AF=0.500;AN=2;BaseQRankSum=0.366;DB;DP=358;Dels=0.00;FS=7.738;HaplotypeScore=45.9328;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=0;MQRankSum=0.483;QD=14.14;ReadPosRankSum=0.820 GT:AD:DP:GQ:PL 0/1:178,180:358:99:5090,0,5314
The first variant is filtred by the "LowQD filter" ( QD = 1.22 < 1.5) whereas it seems to be good. Indeed : QD=QUAL/DP = 32729.73/6710 = 4.87.
When I calculate other QD for other variant in the same file, the result is good.
So, why GATK indicates a wrong QD value ? (I did the Unified Genotyper twice, and the results are the same).
Thank you for your answer. Cecile