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2vcf - convert raw 23andme or ancestry.com data to VCF

The VCF is a widely adopted format for storing detailed data about genetic variation. Services like 23andme and ancestry.com offer to genotype customers at less than a million well-characterized sites in the human genome. It is possible to obtain the raw data collected by these sites, but the raw data are provided in a minimal format, which is not trivial to enrich and transform into the VCF format. 2vcf converts the raw output from 23andme or ancestry.com into a gzipped VCF file. The output vcf is populated with human variant data, which includes all alternate alleles, annotations, etc.

In order to build 2vcf, the golang build tool is required. On os x use homebrew to install it brew install go.

Build 2vcf by checking out the source repo, entering the directory cd 2vcf, and running the make file make. Build for windows by using make windows.

Convert your raw data by running the utility ./2vcf --input-file my-raw-data.zip --output-file my-personal-genotypes.vcf.gz. Running the utility from another location works as well, but remember to specify the path to the reference data as well --vcf-ref /home/me/git/2vcf/reference.vcf.gz.

Please report any errors or difficulties with the utility.