Bivartect: Accurate and memory-saving breakpoint detection by direct read comparison

Abstract

Motivation: Genetic variant calling with high-throughput sequencing data has been recognized as a useful tool for better understanding of disease mechanism and detection of potential off-target sites in genome editing. Since most of the variant calling algorithms rely on initial mapping onto a reference genome and tend to predict many variant candidates, variant calling remains challenging in terms of predicting variants with low false positives. Results: Here we present Bivartect, a simple yet versatile variant caller based on direct comparison of short sequence reads between normal and mutated samples. Bivartect can detect not only single nucleotide variants but also insertions/deletions, inversions and their complexes. Bivartect achieves high predictive performance with an elaborate memory-saving mechanism, which allows Bivartect to run on a computer with a single node for analyzing small omics data. Tests with simulated benchmark and real genome-editing data indicate that Bivartect was comparable to state-of-the-art variant callers in positive predictive value for detection of single nucleotide variants, even though it yielded a substantially small number of candidates. These results suggest that Bivartect, a reference-free approach, will contribute to the identification of germline mutations as well as off-target sites introduced during genome editing with high accuracy.