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→A. Convert dosage file into VCF format
=== A. Convert dosage file into VCF format ===
Use the wrapper program "dose2vcf" to convert your doseage output to pseudo VCF format. Download the tool from [http://wwwcsg.sph.umich.edu/csg/cfuchsb/dose2vcf_v0.5.gz here]. If you used rs numbers during imputation, you can find mapping tables ready for dose2vcf [http://wwwcsg.sph.umich.edu/csg/cfuchsb/mapping_rs_ALL.GIANT.phase1_release_v3.20101123.tgz here (214 Mb) ]
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Note that for longer chromosomes, the program is quite memory intensive. In this case, please convert dosages in shorter sections of the chromosome. For example, if the imputation was performed by sections, then convert these sections to vcf first, and then merge the vcf files together using vcftools [http://vcftools.sourceforge.net/docs.html#concat vcf-concat]:
=== B. bgzip and tabix VCF files ===
