Gwas With Impute2 Output (3 Probability Format)

Question

[Joey]

I was given a huge IMPUTE2 output file (around 70GB) which is is 3 probability format. Is there any software/tool which will read in data of the type, perform QC and do a GWAS?

Alternatively, is there anyway to convert this file format to PED/MAP. GTOOL is not working in my case.

Thanks,

-Joey

[zx8754]

SNPTEST? Link