Entering edit mode
8.2 years ago
dr.genetics
▴
60
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?
