I would like to take a second opinion regarding a variant with DP =17. The variant is in a very high GC content area so the low coverage is reasonable.
I do hard filtering because I have few samples for VQSR, I thinks it is okay according to GATK hard filtering, the values are as follows:
AC=1;AF=0.500;AN=2;BaseQRankSum=0.892;ClippingRankSum=0.000;DP=17;ExcessHet=3.0103;FS=10.843; MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=2.81;ReadPosRankSum=-1.534; SOR=2.795 GT:AD:DP:GQ:PL 0/1:14,3:17:76:76,0,506
I am worried because AD is 14,3 which means only 3 reads only support the ALT? is it safe to accept it as a het variant. The variant is very interesting based on our data, so I don't wanna discard without a strong reason.
Any comments, how do you think? with many many thanks