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Switch awk to bcftools once regression is fixed

Open TedBrookings opened this issue 2 years ago • 0 comments

Minor refactoring

A regression introduced in bcftools version 1.14 caused the SingleSampleFiltering.wdl task FilterVcfBySampleGenotypeAndAddEvidenceAnnotation to fail. I made a work-around using awk, but once that regression is addressed, the usage of bcftools should be restored (faster, more concise, easier to maintain). The instructions for restoring it are in comments withing the command block of the task.

Related bcftools issue: https://github.com/samtools/bcftools/issues/1733

TedBrookings avatar Jun 10 '22 13:06 TedBrookings