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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
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parallel sentieon intervals and fix indel snps #207

Closed erikenbody closed 1 week ago

erikenbody commented 1 week ago

two changes:

  1. long overdue parallelization for the filter_vcfs step of the sentieon model. just use gnu parallel with the -L flag, then combine resulting VCFs
  2. the snps within indel filter in postprocessing wasn't exactly correct. Switching to using -T instead of -R otherwise they get interpreted as regions