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HaplotypeCaller and 1/1:0,0:0:18:383,18,0
We have a single sample which variant is called by HaplotypeCaller. We got a variant which has AD as 0,0, DP 0, however, GT is 1/1. The variant line is:
10 134726068 . TC T 345.80 PASS AC=2;AF=1.00;AN=2;DP=32;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=10.81;SOR=0.693;set=variant2 GT:AD:DP:GQ:PL 1/1:0,0:0:18:383,18,0
I read the following link:
Just want to make sure whether this is the reason, because our case is a homozygosity variant. By the way, for clarify, the DP in the INFO field is not filtered (PCR dups, mapping quality, etc.), but the AD and DP in the sample field are all filtered? At the example you mentioned at the page, Both DP in INFO and SAMPLE field are 10. Is that the DP in SAMPLE field should be 0?