Do we discard variants with repetitive regions and do these masks mean repetition?

Question

[Dayna]

Hi

Do we discard variants that has repetitive parts? For example in this image, are these black masks of tandem repeats means I should discard the variant here? https://ibb.co/cmqBuc

thanx

[h.mon]

I think you don't necessarily have to mask these regions, but should be aware of them, and consider it when filtering the variants. Look at the comments on this thread, or this thread at the GATK forum.