Minimac3 to Mach2dat for imputation

Question

[xliu4255]

Hi everyone,

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.

Answer 1

[melfaramawi1]

Use Dosageconvertor "http://genome.sph.umich.edu/wiki/DosageConvertor" to convert the VCF file to mldose and mlinfo files.

For Match2dat: For covariates, you have to construct a dat file. The dat file will have the following letters C=covariate and T=Trait . You must make sure that your ped file is constructed so that the following variables are included: SNP or chr:pos ID ID.family Sex Covariate1 Covariate2 .... Trait

[xliu4255]

Thanks for your help:)