Hi Every one
If we have an interesting variant in a very high GC content, so we expect low coverage anyway. The variant has depth 18 with AD 15,3.
Is having 3 reads enough to say there is a variant at this site? GQ = 78.
Given that the all the reads has
58-60 Mapping quality,
All the bases quality are between
and the variant passes the hard filtering of GATK pipeline, like QD =2.7 (greater than 2) , FS <10 , SOR <3 and all other metrics given GATK suggestions pass..etc.