Question: Calculate linkage disequilibrium from Hudson's ms simulated binary data
0
gravatar for Mr Locuace
4.5 years ago by
Mr Locuace100
Chile
Mr Locuace100 wrote:

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

001010 
110101 
010100 
001010 
010100

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 !

r2 ld cosi ms software hudson • 1.2k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 4.5 years ago by Mr Locuace100

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 REPLYlink written 4.5 years ago by microfuge1.9k

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

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Mr Locuace100
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