Entering edit mode
6 weeks ago
abhishekghadge
▴
30
When using Strelka on sequenced bams, the VCF file contains many variants with very low allelic depth.
When I try to sequence the sample again and then generate the VCF there is a lot of mismatch between the 2 generated VCFs. This problem occurs at high frequencies in variants with low allelic depth ( 1, 2) and steeply drops off above this limit to almost non-existent.
When considering these Variants, should we ignore or filter out variants with low allelic depth?
Has anyone else encountered this issue and how did you deal with this issue?
