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Genetic map for chromosome X that shows recombination rates?

I am doing some phasing using SHAPEIT.

SHAPEIT takes a genetic map as input which shows:

"Recombination rates between SNPs are provided via a genetic map that specifies the genetic position of the SNPs in cM".

SHAPEIT has a link to a set of genetic maps for all autosomes (now broken, but found on wayback machine):

https://web.archive.org/web/20180130092014/http://www.shapeit.fr/files/genetic_map_b37.tar.gz

This genetic map has has for each autosome a 3 column text file with the following headers:

position, COMBINED_rate(cM/Mb), Genetic_Map(cM)

But no chromosome 23.

  1. Does anyone know where I could get a genetic map that has chromosome 23

  2. If not does anyone know where I might look to begin making my own?

shapeit phasing
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updated by Kevin Blighe Kevin Blighe • written by curious curious

1 answer

You can download the chrX genetic map information from here: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html

If you cannot access that, I also host the genetic map information for all chromosomes on my personal storage space, including legend and hap files, too; so, that can be made available if needed, too.

Kevin

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written by Kevin Blighe Kevin Blighe

It seems so far that I can access the link, the file is huge though, once I get it downloaded I will take a look. Thank you!

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written by curious curious

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