RT Journal Article
SR Electronic
T1 Thousands of missing variants in the UK BioBank are recoverable by genome realignment
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 868570
DO 10.1101/868570
A1 Jia, Tongqiu
A1 Munson, Brenton
A1 Allen, Hana Lango
A1 Ideker, Trey
A1 Majithia, Amit R.
YR 2019
UL http://biorxiv.org/content/early/2019/12/10/868570.abstract
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.