bimmanglesnpids

Documentation

Overview

bimmanglesnpids is designed to handle a specific situation where you want to mangle rsids intentionally. This arises when subsetting from a format (e.g., bgen) which does not have expressive tools for requesting not only rsID but also ref and alt allele (since multiallelics are so common). So, this tool allows you to make sure that the SNPs in your BIM file contain not only a matching rsID, but also a matching ref and alt allele from a lookup file. And, if not,