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Calculating linkage using dosage data?

ebware
in Genetics

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Hey everyone. I'm trying to find a program that can calculate LD from dosage data. This has been a fruitless search. I'm trying to prune GWAS results to eliminate loci that are in LD > 0.80 using LD calculated from MY DATA and not from HapMap or 1000G.

 

Any suggestions?

 

Thanks

 

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