RT Journal Article
SR Electronic
T1 Benchmarking small variant detection with ONT reveals high performance in challenging regions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.10.22.350009
DO 10.1101/2020.10.22.350009
A1 Peter L. Møller
A1 Guillaume Holley
A1 Doruk Beyter
A1 Mette Nyegaard
A1 Bjarni V. Halldórsson
YR 2020
UL http://biorxiv.org/content/early/2020/10/23/2020.10.22.350009.abstract
AB Background The development of long read sequencing (LRS) has led to greater access to the human genome. LRS produces long read lengths at the cost of high error rates and has shown to be more useful in calling structural variants than short read sequencing (SRS) data. In this paper we evaluate how to use LRS data from Oxford Nanopore Technologies (ONT) to call small variants in regions in- and outside the reach of SRS.Results Calling single nucleotide polymorphisms (SNPs) with ONT data has comparable accuracy to Illumina when evaluating against the Genome in a Bottle truth set v4.2. In the major histocompatibility complex (MHC) and regions where mapping short reads is difficult, the F-measure of ONT calls exceeds those of short reads by 2-4% when sequence coverage is 20X or greater.We develop recommendations for how to perform small variant calling with LRS data and improve current approaches to the difficult regions by re-genotyping variants to increase the F-measure from 97.24% to 98.78%. Furthermore, we show how LRS can call variants in genomic regions inaccessible to SRS, including medically relevant genes such as STRC and CFC1B.Conclusions Although small variant calling in LRS data is still immature, current methods are clearly useful in difficult and inaccessible regions of the genome, enabling variant calling in medically relevant genes not accessible to SRS.Competing Interest StatementGuillaume Holley, Doruk Beyler and Bjarni V. Halldórsson are employees of deCODE genetics/Amgen Inc.