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Thousands of missing variants in the UK BioBank are recoverable by genome realignment

Tongqiu Jia, Brenton Munson, Hana Lango Allen, View ORCID ProfileTrey Ideker, View ORCID ProfileAmit R. Majithia
doi: https://doi.org/10.1101/868570
Tongqiu Jia
1Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Brenton Munson
1Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Hana Lango Allen
2Medical Research Council Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
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Trey Ideker
1Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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  • For correspondence: tideker@ucsd.edu amajithia@ucsd.edu
Amit R. Majithia
1Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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  • ORCID record for Amit R. Majithia
  • For correspondence: tideker@ucsd.edu amajithia@ucsd.edu
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Abstract

The UK Biobank is an unprecedented resource for human disease research. In March 2019, 49,997 exomes were made publicly available to investigators. Here we note that thousands of variant calls are unexpectedly absent from the current dataset, with 641 genes showing zero variation. We show that the reason for this was an erroneous read alignment to the GRCh38 reference. The missing variants can be recovered by modifying read alignment parameters to correctly handle the expanded set of contigs available in the human genome reference.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 10, 2019.
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Thousands of missing variants in the UK BioBank are recoverable by genome realignment
Tongqiu Jia, Brenton Munson, Hana Lango Allen, Trey Ideker, Amit R. Majithia
bioRxiv 868570; doi: https://doi.org/10.1101/868570
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Thousands of missing variants in the UK BioBank are recoverable by genome realignment
Tongqiu Jia, Brenton Munson, Hana Lango Allen, Trey Ideker, Amit R. Majithia
bioRxiv 868570; doi: https://doi.org/10.1101/868570

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