Question: How does plink calculates linkage disequilibrium (r2) in unphased data?
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gravatar for serpalma.v
17 months ago by
serpalma.v60
Germany
serpalma.v60 wrote:

Hello

when I pass a vcf file to plink, it can calculate the linkage disequilibrium (r2) even though the data is not phased. How is this possible when the haplotype frequencies for SNP pairs are not known?

Thanks!

sequencing snp plink • 726 views
ADD COMMENTlink modified 17 months ago by chrchang5237.6k • written 17 months ago by serpalma.v60
0
gravatar for chrchang523
17 months ago by
chrchang5237.6k
United States
chrchang5237.6k wrote:

For each SNP, you can write a {0, 1, 2}-valued vector of REF allele counts. The unphased-r2 reported by plink is the square of the sample Pearson correlation between these two vectors.

ADD COMMENTlink modified 17 months ago • written 17 months ago by chrchang5237.6k

Would the result have the same interpretation as r^2=D^2/(p1p2q1q2)?

ADD REPLYlink written 17 months ago by serpalma.v60
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