What does the R2 of EAGLE imputation mean?

The dose.vcf file produced by EAGLE has the following format:

1   249240051   1:249240051 T   TA  .   PASS    AF=0.62563;MAF=0.37437;R2=0.00065   GT:DS   1|1:1.251
1   249240099   1:249240099 T   TA  .   PASS    AF=0.57255;MAF=0.42745;R2=0.00031   GT:DS   1|1:1.145
1   8722507 1:8722507   A   G   .   PASS    AF=0.79200;MAF=0.20800;R2=0.20230   GT:DS   1|1:1.584

My question is about the R2 here: what are these R2 values? It looks like the smaller the R2, the better the imputation?

snp software error sequencing genome

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written 9.8 years ago by dr.genetics

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