Where can I find the genetic map for GRCh37 to phase genotypes on SHAPEIT2
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9 weeks ago
Khaleesi95 ▴ 30

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.

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

Many thanks!

genetics genetic map shapeit2 • 266 views
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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?

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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...

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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

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