Minimac VCF conversion

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A wrapper program "dose2vcf" can be used to convert your doseage outputs from Minimac/Minimac2 or Impute2 to VCF format. This program can be downloaded from http://www.sph.umich.edu/csg/cfuchsb/dose2vcf_v0.5.gz.

To run the program for Minimac/Minimac2 imputed data, use the following command:

./dose2vcf --dose [.dose file] --info [.info file] --out [output file prefix]

For example, for Minimac imputed chromosome 1 data from GCKD:

./dose2vcf --dose GCKD.GWAS.1KG.imp.chr1.dose --info GCKD.GWAS.1KG.imp.chr1.info --out out/GCKD.GWAS.1KG.imp.chr1

The output VCF file is at:

out/GCKD.GWAS.1KG.imp.chr1.vcf

If you used rs numbers during imputation, you can get mapping tables ready for dose2vcf from http://www.sph.umich.edu/csg/cfuchsb/mapping_rs_ALL.GIANT.phase1_release_v3.20101123.tgz (214 Mb) and use the option --rs with the mapping file when running dose2vcf.