search

NBISweden / GenErode

GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
GNU General Public License v3.0
23 stars 7 forks source link

Filtering for biallelic sites does not remove sites with fixed derived variants #55

Open verku opened 1 year ago

verku commented 1 year ago

https://github.com/NBISweden/GenErode/blob/main/workflow/rules/9_merge_vcfs.smk#L266C23-L266C42

This command does not remove sites that are coded as heterozygous sites but are fixed derived sites (for ALT), i.e. monomorphic, which are common when mapping to a derived genome.

verku commented 3 months ago

A Snakemake workflow to process snpEff output and the merged VCF file has been added to the dev branch. In this workflow, fixed derived alleles are removed from the merged VCF and subsequently from the snpEff VCF files.