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
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Update gerp_derived_alleles.py to work with phased genotypes #67
I was getting an error and noticed that it crashes when there are genotypes in the vcf file that are phased (0|0 instead of 0/0). So I just modified line 138 to :
From a user contacting us:
I was getting an error and noticed that it crashes when there are genotypes in the vcf file that are phased (0|0 instead of 0/0). So I just modified line 138 to :
focal_genotype = re.split(r"/||", row[samplename])
and imported re at the beginning of the script:
import re