Dear Biostars community,
I am trying to run "Bevimed" - https://cran.r-project.org/web/packages/BeviMed/vignettes/Intro.html. A Bayesian approach to rare variant analysis on a case control cohort.
I have the cases and controls in a merged per chromosome format as well as in plink binary files.
As part of using Bevimed there are is a need to create a genotype matrix file:
- an N by k integer matrix of allele counts for N individuals at k rare variant sites
I was wondering if there was a method of generating this matrix using existing tools? Does plink --recode12 do the same thing?
Many thanks for your help