PT  - JOURNAL ARTICLE
AU  - Jia, Tongqiu
AU  - Munson, Brenton
AU  - Allen, Hana Lango
AU  - Ideker, Trey
AU  - Majithia, Amit R.
TI  - Thousands of missing variants in the UK BioBank are recoverable by genome realignment
AID  - 10.1101/868570
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 868570
4099  - http://biorxiv.org/content/early/2019/12/10/868570.short
4100  - http://biorxiv.org/content/early/2019/12/10/868570.full
AB  - 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.