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Thousands of missing variants in the UK BioBankare recoverable by genome realignment

By Tongqiu Jia, Brenton Munson, Hana Lango Allen, Trey Ideker, Amit R. Majithia

Posted 10 Dec 2019
bioRxiv DOI: 10.1101/868570 (published DOI: 10.1111/ahg.12383)

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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