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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

MarkDuplicates memory issues #30

Closed cademirch closed 2 years ago

cademirch commented 2 years ago

@sjswuitchik has run into out of memory issues with MarkDuplicates. For some reason, the picard CLI does not have a
--java-options argument like GATK, so there does not appear to be a direct way to give the JVM more memory. The Snakemake MarkDuplicates wrapper seems to be able to do this, but I'm not entirely sure how.