Convert Impute2 Output Into Most Likely Genotypes

Question

[winnie628]

Hi all, I have a question about how to convert the IMPUTE2 output into most likely genotypes (either in 0,1,2 format or A/T/G/C format). Is there a program or function available to do that? If not, is it realistic to use R to do the conversion? Thanks!

Answer 1

[Joey]

You can use GTOOL to convert IMPUTE2 output to PLINK ped/map format and use the --recodeA command in PLINK to get the data in to 0/1/2 format.