Hello everyone!
I am using GATK as a new pipeline for our laboratory. I'm getting some results from HaplotypeCaller that I have some questions about.
In particular, I'm wondering why I have the number of comma-delimited values in the AD field.
Here is and example output: GT:AD:DP:GQ:PL:SB 0/1:19,3,0:22:26:26,0,625,83,634,717:10,9,2,1
I understand this means I have a heterozygous call at this position. (0/1). But I'm wondering why I have 3 values in the AD field (19, 3, 0). My reading of the samtools output suggests that there could be 4 outputs (forward ref, reverse, ref, forward alt, and reverse alt). Why do I only have 3 results?