Use mosdepth d4tools to facilitate coverage calcs

harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

MIT License

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Use mosdepth d4tools to facilitate coverage calcs #59

Closed tsackton closed 2 years ago

tsackton commented 2 years ago

This pull request changes the way we do coverage calculations, to use mosdepth and d4tools instead of relying on bedtools unionbedgraph, which can be very slow for large sets.