I have some imputed data by using Minimac3, which include .vcf, .m3vcf, .info, .erate, .rec these 5 formats. I would like to use mach2dat for association analysis, but it would require .ped, .dat, mlinfo. mldose files as input. I think I can convert .vcf to .ped and .map by using PLINK. But how can I get the .dat, .mlinfo, .mldose files? Use some Linux command to transform .info to mldose? Creat .dat manually? Also I don't know how read .mldose file... And if I want to add some covariates, where should I put them? The last column of the .ped file?
I really appreciate any help.