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Calculating genetic distance from VCF to MAP format

I have a VCF from which I got the .ped and .map files using plink. However, the genetic distance (3rd column) has been set to 0. I want the map file to include the genetic distances. For my analysis, I am assuming a constant recombination rate of 15 kb/Cm.

Does plink have a command where you can provide the recombination rate so the output map file has the genetic distances? I was not able to find how the calculation is done from their manual.

I have thought about calculating them manually, but I am slightly confused with the formula -

If I have a VCF file having the following SNPs...

Chrom_01_v3     613
Chrom_01_v3     714
Chrom_01_v3     779

is it 714/15k or (714 - 613)/15k? In the latter case, since I have SNPs that are quite close to one another, I am getting genetic distances that are too small for my analysis.

My goal is to do IBD through the R package isoRelate which requires the input as .ped and .map format. My end goal is to get a Manhattan Plot.

population genomics
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updated by chrchang523 chrchang523 • written by VBer VBer

1 answer

https://www.cog-genomics.org/plink/1.9/input#cm_map

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written by chrchang523 chrchang523

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