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Converting a 23andMe Raw Genetic File to VCF

23andMe customers can download their raw genetic data, following these instructions.


However, this data comes in a propietary 23andMe format.


The 23andMe file is called something like (the exact file name format may vary).


Here, we explain how to convert the file to the standard VCF format.


Step 1: Download a reference file - any version of hg19 or GRCh37 will do, for example this one: hs37d5.fa.gz. This file is quite large: appoximately 900MB.

Step 2: Compress your 23andMe file with Genozip:


Step 3: Convert the file to VCF

genocat -e hs37d5.fa.gz --vcf genome_John_Doe_v3_Full_20190101201010.genozip --output mydata.vcf.gz

Note: the output file (mydata.vcf.gz in the example above) is compressed into .gz format if the file name ends with .gz.

Limitations: Indel variants (‘DD’ ‘DI’ ‘II’) as well as uncalled sites (’–’) are discarded



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