PacificBiosciences / pb-human-wgs-workflow-snakemake

Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
BSD 3-Clause Clear License
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Remove slivar filters for sex chromosome variants #131

Closed williamrowell closed 5 months ago

williamrowell commented 1 year ago

segregating_dominant_x was redundant with segregating_dominant

The more general function checks the chromosome before applying the more specific function. slivar-functions.js

Also, expression was checking for chrX, so these would have failed for hs37d5.

Related to #127

williamrowell commented 1 year ago

~I need to add denovo and x_denovo now.~

I remember the logic here now. We're using the more general --family-expr instead of --trio so we're not doing anything special to find de novo variants with slivar.