Can someone please recommend any tool that I can use for IMPUTE2 data extraction? So far, I have tried Gtool, but it's very slow. I want to extract data for > 50K SNPs. I have also tried PLINK2 but I am afraid that I will loose IMPUTE2 probability data because PLINK2 convert everything to PLINK format and convert the IMPUTE2 probabilities to genotype call using with the best guess.
Thanks for your help.