aryarm / as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq
MIT License
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extract heterozygotes from the vcf before converting to h5 files #63

Open aryarm opened 3 years ago

aryarm commented 3 years ago

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?

aryarm commented 3 years ago

actually, it turns out that extracting heterozygotes from the vcf is the last step in the variant calling pipeline

so we should