Hi I'm using the Haplotypecaller 3.4 in my pipeline, and I've detected this Issue. Depth is 37, with such a huge quality and when looking at the last column I see a GT 1/1 suported by an AD of 0,0 and a DO o 0.
Have you noticed this? If so, has this been corrected in 3.5?
It is giving me problems with other steps as depth is 0.
chr11 10823576 . C CACACTCCTAAAATAGTTTCATGTTTTAATAGCAAATGAAATCACATATATTGCAGAATTTAACATTTGTTGCCTAA 5199.77 PASS DP=37;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,0:0:99:5180,332,0