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evotools / hapbin

Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)
GNU General Public License v3.0
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map file format requires genetic distance but I only have physical distance #63

Open Yasirnawaz89 opened 3 years ago

Yasirnawaz89 commented 3 years ago

Hi,

I am using Hapbin for WGS in cattle. I do not have genetic distance because I do not know recombination rates. Can I just use divide physical location by a 1 million to get the genetic distance for your software?

Secondly, dimensions of my largest chromosome are 443000 SNPs and 13 K animals and it is taking around 12 days to calculate his of one chromosome. Is there a way I can make it more efficient?

Thanks

prenderj commented 3 years ago

Hi

Ideally would use genetic distance, but yes for mammals people often assume 1cM/Mb when there is no recombination map available (including us https://www.nature.com/articles/s41467-020-18550-1).

13,000 is a lot of samples so it would potentially take some time. However you will probably find if calculate iHS on a random subset of the samples the results are largely the same as the iHS on the total dataset but will run faster. You can test this by taking various random subsets of different sizes and see how the iHS values converge on given values. It will likely plateau at a much smaller sample size.

Hope that helps.

James

On Fri, 8 Jan 2021 at 17:04, Muhammad Yasir Nawaz notifications@github.com wrote:

Hi,

I am using Hapbin for WGS in cattle. I do not have genetic distance because I do not know recombination rates. Can I just use divide physical location by a 1 million to get the genetic distance for your software?

Secondly, dimensions of my largest chromosome are 443000 SNPs and 13 K animals and it is taking around 12 days to calculate his of one chromosome. Is there a way I can make it more efficient?

Thanks

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