Add subcommand to mask sequences #4481
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jeizenga
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Changelog Entry
To be copied to the draft changelog by merger:
vg maskis a new subcommand that can hard mask sequences in a graphDescription
Coordinated with vgteam/libbdsg#208 and vgteam/libhandlegraph#99. I'll update this PR to the merged commit when those are merged.
This PR is a new subcommand that allows you to hard mask sequences in GBZs and libbdsg graphs using a provided BED file. The change is motivated by known assembly errors in GRCh38. Masking these sequences during mapping should significantly narrow the gap in variant calling performance to DRAGEN on the CMRG panel. Another possible use case is masking the chrY PAR.