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How does plink calculates linkage disequilibrium (r2) in unphased data?

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!

plink snp sequencing
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updated by chrchang523 chrchang523 • written by serpalma.v • serpalma.v

1 answer

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.

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written by chrchang523 chrchang523

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

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written by serpalma.v • serpalma.v

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