GenomePrep

Incentive

Two major forces have contributed to the fast growth of human genetic data. One from medical research supported by governments and academic institutes; the other from direct-to-consumer (DTC) sequencing companies. While the former benefits from meticulously designed sequencing standards and quality control procedures, the latter comes in various formats and sequencing methods which are subject to changes over time and the particular needs of various companies. Thanks to the general public who shared their DNA data without constraint, we were able to review over 7,000 genomes made public between 2011 and 2020, produced by over six DTC companies, from OpenSNP and PGP.

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Summary

The open-source GenomePrep tool-kit, developed on the goodwill of open genome data, addresses the problem of processing raw DTC DNA data in the context of the present: genotype arrays. The output of GenomePrep are DNA datafiles of homogenous formats (23andMe-like or vcf), which enable further research analysis (example). A single combined data-freeze of genomes that passed checks is also available below.

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Downloads

Source code can be found on Github. There is a copy of related files on Zenodo .

Quick check variants seen in the OpenSNP genomes: openSNP.bim

Additional data support can be requested by contacting my email.

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Publication

C. Lu, B. Greshake Tzovaras, J. Gough, A survey of direct-to-consumer genotype data,and quality control tool (GenomePrep) for research, Computational and Structural Biotechnology Journal(2021), doi: https://doi.org/10.1016/j.csbj.2021.06.040

Please cite both the paper above and the OpenSNP or PGP accordingly when using data above.