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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
63 stars 30 forks source link

Feat optional dedup #173

Closed cademirch closed 2 months ago

cademirch commented 2 months ago

adds optional dedup. default is to mark duplicates. if skipping marking duplicates, need to add --notemp when executing snakemake to preserve bams.