for bcftools concat we are using all for the --rm-dups argument.
What was the original reasoning for using this?
We may have to use none . Otherwise, multliallelic positions (or multiple variants with same position), only one mutation is retained following vcf concatanation.
bcftools_params:
allow_overlaps: true
rm_dups: all # <--- here
for bcftools concat we are using
allfor the--rm-dupsargument.What was the original reasoning for using this?
We may have to use
none. Otherwise, multliallelic positions (or multiple variants with same position), only one mutation is retained following vcf concatanation.