Calculate linkage disequilibrium from Hudson's ms simulated binary data

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7.7 years ago

Mr Locuace ▴ 160

Hello, I have simulated genetic data from Hudson's ms (and COSI) software in this form:

where 0 and 1 represent the ancestral and derived allele, respectively. Each line represents a chromosome from an individual, whereas each column represents a SNP. Is there any way of calculating LD-related measures from this data, such as D' or r2?. I know how to do it from real genetic data (A,C,G,T) but I have not found how to do it from binary (0,1) data. Any suggestion is very welcome !

LD r2 Hudson ms software cosi • 2.0k views

ADD COMMENT • link updated 7.6 years ago by Biostar 20 • written 7.7 years ago by Mr Locuace ▴ 160

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For the number of recombination events I use RecMin. The input file format is quite similar to the data you have. http://www.stats.ox.ac.uk/~myers/RecMin.html

ADD REPLY • link 7.7 years ago by microfuge ★ 1.9k

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Thanks very much @microfuge .I will try it !. Can it calculate r2 or D'?

ADD REPLY • link 7.7 years ago by Mr Locuace ▴ 160

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