Hi GATK team
I ran HC joint calling and found out that some non-reference alleles didn't appear in the vcf. Here are how these sites looks like:
Most of these allele have VAF =1 and reside on the region of high sequencing depth with relatively poor alignments (seems to be germline variant).
My first guess is that they are disgarded by early steps of HC. However, I went through documentation of HC procedure and didn't find a definitive answer of how exactly they are discarded. Can anyone share some insights on this? Thanks a lot