Question: (Closed) Creating a genotype matrix
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gravatar for omid.alavijeh
4 months ago by
omid.alavijeh40 wrote:

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

genotype bcftools • 98 views
ADD COMMENTlink written 4 months ago by omid.alavijeh40

Hello omid.alavijeh!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 4 months ago by genomax84k
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