Where can I find the genetic map for GRCh37 to phase genotypes on SHAPEIT2

Question

[Khaleesi95]

Hi guys, I need to phase my genotypes using SHAPEIT2 software. I'm using the following indications: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#prephasing.

I need to run the following command line:

shapeit -B gwas \
    -M genetic_map.txt \
    -O gwas.phased

Concerning the -M option, I need a genetic map, and precisely I need the HapMap b37 genetic map.

I've tried to download it at the following link: http://www.griv.org/shapeit/pages/geneticmap.html but I haven't succeeded in downloading it...

Someone knows where I can find this file for phasing my genotypes?

Many thanks!

[4galaxy77]

Hi Khaleesi, shapeit2 is quite old now (actually ~ a decade old) and there several much more efficient and accurate methods available. Is there a reason why you're using such an old method?

[Khaleesi95]

Hi 4galaxy77, my boss suggested me to use shapeit2 to phase as we have the software already installed on our cluster...so it'd be better if I used it. However, I don't know where I can find the genetic map...it seems not be found...

[4galaxy77]

That's understandable. You could install shapeit4 using conda here using conda install -c bioconda shapeit4 if conda is already installed. It will save you a lot of time in the long run, as shapeit4 is a lot faster than shapeit2 and also more accurate. You can find the genetic maps here https://github.com/odelaneau/shapeit4/tree/master/maps

[Khaleesi95]

Great, thank you for your answer! Yeah, I'll try to install shapeit4 through conda!