2vcf

in order to improve individual sovereignty over genetic/genomic information, facilitate a deeper understanding of biology and computation, and promote shared meaning, openb.io provides 2vcf under the MIT license. 2vcf will convert raw genotype data exports from 23andme or Ancestry.com into VCF format.

2vcf produces a VCF that contains annotations from dbSNP build 151 on GRCh37.p13. these annotations include allele frequencies from various sources including 1000 Genomes and ExAC, RefSeq gene annotations, and functional class of the variant.

the source VCF for dbSNP build 151 weighs in at around 15GB. the sites assayed by personal genomics companies are but a tiny fraction of the totality of dbSNP sites. so I make available a reference version of the dbSNP VCF which has been filtered down to those sites likely to be contained in your exported 23andme or Ancestry.com exported raw data. for more details on which sites are included and why, see this post on version 3.0 of the reference.

usage

  1. download the appropriate binary for your architecture from the most recent github release. un-tar the contents after downloading.

    wget https://github.com/plantimals/2vcf/releases/download/v0.5/2vcf_0.5_Darwin_amd64.tar.gz
    tar -zxf 2vcf_0.5_Darwin_amd64.tar.gz
    
  2. download the reference vcf https://openb.io/2vcf/2vcf-v3.0.vcf.gz

    wget https://openb.io/2vcf/2vcf-v3.0.vcf.gz
    
  3. download your raw genotype data from 23andme or Ancestry.

  4. now run the 2vcf binary with the appropriate options:

    ./2vcf conv 23andme --ref path/to/2vcf-v2.0.vcf.gz \
    --input path/to/my/raw/genotypes.zip \
    --output my-personal-annotated.vcf.gz