Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

Peter Edge and Vikas Bansal ()
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Peter Edge: University of California, San Diego
Vikas Bansal: University of California, San Diego

Nature Communications, 2019, vol. 10, issue 1, 1-10

Abstract: Abstract Whole-genome sequencing using sequencing technologies such as Illumina enables the accurate detection of small-scale variants but provides limited information about haplotypes and variants in repetitive regions of the human genome. Single-molecule sequencing (SMS) technologies such as Pacific Biosciences and Oxford Nanopore generate long reads that can potentially address the limitations of short-read sequencing. However, the high error rate of SMS reads makes it challenging to detect small-scale variants in diploid genomes. We introduce a variant calling method, Longshot, which leverages the haplotype information present in SMS reads to accurately detect and phase single-nucleotide variants (SNVs) in diploid genomes. We demonstrate that Longshot achieves very high accuracy for SNV detection using whole-genome Pacific Biosciences data, outperforms existing variant calling methods, and enables variant detection in duplicated regions of the genome that cannot be mapped using short reads.

Date: 2019
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DOI: 10.1038/s41467-019-12493-y

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