This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Allele Depth = '0,0' and DP = '0' but the mutation was passed by filter
There is a question if anyone can explain to me how this variant calling was made, and why it was passed by filter.
A variant information in filtered VCF is:
10 118265356 . G A 152.03 PASS AC=2;AF=1.000;AN=2;DP=0;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.000;MQ=0.00;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,0:0:12:180,12,0
My gatk version is v3.3.
Thanks for any help.