Creating a genotype matrix for BeviMed

Question

[tacrolimus]

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

[German.M.Demidov]

This is an interesting question as for me who just starts to work with this tool. I suppose it has to be created manually with 0 for the allele with major frequency, 1 for heterozygous minor variant, 2 for homozygous. I'll put an update once I'll be able to run it.

UPD: looks like I was right, this is from the paper;

"Suppose k rare variants are under consideration (typically in a particular genomic region) and the genotype for individual i at variant j is coded in the ith row and jth column of the genotype matrix G. A genotype of 0 or 2 denotes homozygosity for the common or minor allele, respectively, and a genotype of 1 denotes heterozygosity."

[tacrolimus]

Thanks German, would there be an easy way of making such a file from a VCF?