Homozygotes aren't useful in allele-specific analyses, so we discard them in the counts subworkflow. But discarding them upstream, even before running WASP, might significantly speed up execution of the pipeline. So are there any downsides to this?
actually, it turns out that extracting heterozygotes from the vcf is the last step in the variant calling pipeline
so we should
[ ] add a comment to the wasp and counts configs (and their documentation) that encourages users to extract heterozygotes from their VCFs before passing the variants into our pipeline
instead of downstream in the counts subworkflow
Homozygotes aren't useful in allele-specific analyses, so we discard them in the counts subworkflow. But discarding them upstream, even before running WASP, might significantly speed up execution of the pipeline. So are there any downsides to this?