Where can I find the genetic map for GRCh37 to phase genotypes on SHAPEIT2
0
2
Entering edit mode
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.

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!

genetics genetic map shapeit2 • 265 views
ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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...

ADD REPLY
2
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2143 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6