how to convert pyrho output to cM/Mb

[selasphoruskershaw]

Hi,

I am trying to phase my data in Shapeit4, and need to include recombination rate in units of Cm/Mb, not scaled-recombination per site per generation rate. I also need genetic position in units of cM. Is there any script or equation I can use to do so? I haven't found a script online up to this point. Thank you for any help you can provide.

[jeffspence]

Hello!

There's no script, but it's easy to calculate from the output of pyrho optimize. This issue should be enough to get you on the right track.

Let me know if anything is unclear.

I'll also leave this issue open because I should implement the functionality to produce this in pyrho iteself.

[selasphoruskershaw]

Thanks for your response!

Just to confirm:

If I have a rate output by pyrho at 1.67e-11, is the rate in units of cM/Mb equal to 1.67e-3? And the units in terms of cM 1.67e-9?

Thanks again for your help

[jeffspence]

Yes -- 1.67e-11 recombinations/generation should be 1.67e-3 cM/Mb.

cM/Mb and the pyrho output are both rates -- how frequent is recombination per base pair . In contrast cM is a unit of genetic distance so to get cM you need to sum up the rates times the length of the intervals that they cover.

e.g., say SNP 1 is at 5 cM, SNP 2 is 3 Mb away from SNP 1, and the rate of recombination between them is 1.5 cM/Mb, then SNP 2 is at 5 + 3*1.5 = 9.5 cM

[selasphoruskershaw]

Thank you for your help, I got it working!

One other issue, I'm trying to estimate recombination using pyrho for a phased chromosome, and want to compare it to unphased recombination rates for the same dataset. However, shapeit outputs a .haps and .sample file, and the command to convert these files to vcf appears to be deprecated. Do you know of a workaround or are there any plans to allow for .haps/.sample input in the future? Thank you!

[jeffspence]

Glad to hear it!

Unfortunately, I don't have any plans to implement a parser for .haps and .sample files. I suspect that you should be able to use plink to convert between file formats, but I have not done it myself.