Split chromosomes before joint genotyping

campanam / RatesTools

Pipeline to calculate de novo mutation rates from parent-offspring trios

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Open campanam opened 2 years ago

campanam commented 2 years ago

Increase parallelization by splitting the chr before joint-genotyping. Also prevents wasted effort genotyping chaff.

campanam commented 4 months ago

This would also help WhatsHap phasing which is currently single-threaded by necessity. May necessitate dropping of support for GATK3.