Is it possible to get LD statistics keeping haplotype in mind?
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5.0 years ago

I have SHAPEIT haplotype scaffolds for a 1Mb region. I would like to determine the R2 of pairwises SNPs in a haplotype dependent manner.

Is there an option in PLINK that will produce LD statistics with haplotype in mind?

Or am I missing the point of LD and the results would be the same if the SNPs were not phased?

LD PLINK R2 Haplotype SHAPEIT • 1.2k views
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PLINK 1.x is not able to import phase information. LD statistics which take it into account will be a bit different.

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Could you try separating the haplotypes into different plink files, then calculate it per (haplotype specific) plink file? You might have to do a lot of slicing and dicing, but you might be able to get it done this way.

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