False Homozygous Variant call within a repeat?
I'm hoping you can help resolve the behaviour of HaplotypeCaller with respect to a certain position.
Here's the IGV screenshot, with these filters: MQ>30, filter secondaries and dups. The DP is 14-18 across this deletion.
HC called a TATA deletion in this proband, with this gvcf call:
5 67597220 rs71655141 GTATA G,<NON_REF> 95.14 . DB;DP=12;MLEAC=2,0;MLEAF=1.00,0.00;MQ=57.93;MQ0=0 GT:AD:DP:GQ:PL:SB 1/1:0,3,0:3:10:132,10,0,132,10,132:0,0,1,2
It's calling this as
Clearly this is likely all noise, and a tough region of the genome to make a call in, but i'm curious why the depth is 3, how HC handles the multiple overlapping deletions - ie how it only makes the delTATA call.
I'm using GATK 3.3, and following best practices.