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mbhall88 / NanoVarBench

Evaluating Nanopore-based bacterial variant calling
https://doi.org/10.1101/2024.03.15.585313
MIT License
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Masking repetitive regions #4

Closed mbhall88 closed 6 months ago

mbhall88 commented 8 months ago

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 commented 8 months ago

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

mbhall88 commented 8 months ago

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.