Masking repetitive regions

[mbhall88]

Do we want to mask repetitive regions of the genome - both from the truthset and the callset?

My (naive) way of approaching this would be to just align the genome to itself and mask any position with a depth >1.

[rrwick]

I vote no - don't mask anything. Masking repeats is for short reads 😄

[mbhall88]

Yeah, agreed. This is probably a good test for the variant callers. As was mentioned in this review, variant callers should have strategies for dealing with reads that map to repetitive regions. I think this will be a good test.