This tool has been built in order to allow a user of 23andme to process the raw file format into a format more widely useful across bioinformatics tools, the VCF (see format details).
A reference is included which is limited to only those sites targetted by the 23andme microarray. 23andme recently made the change from build36 (hg18) to build37 (hg19), so any raw files downloaded before August 9, 2012 will be based on the older build36 coordinates. Simply download the raw data again and it will be on the build37 coordinates. If there is a need for build36 support, let me know and I can add that in as an option.
IN/DELs are currently unsupported by this program. Support is planned for the near future.
git clone git://github.com/arrogantrobot/23andme2vcf.git
cd 23andme2vcf
perl 23andme2vcf.pl /path/to/23andme_raw.(zip,txt) /path/to/output.vcf
This tool will work equally well with the compressed raw file (.zip format) or the uncompressed, text file.
The reference contained here-in is a list of reference bases taken from [NCBI build37] (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ "NCBI build37"), which matches those sites included in the 23andme microarray exactly, in order to limit the file size and speed up creation of the VCF.