Somatic variant analysis of linked-reads sequencing data with Lancet.

Abstract

We present a new version of the popular somatic variant caller, Lancet, that supports the analysis of linked-reads sequencing data. By seamlessly integrating barcodes and haplotype read assignments within the colored De Bruijn graph local-assembly framework, Lancet computes a barcode-aware coverage and identifies variants that disagree with the local haplotype structure. Lancet is implemented in C++ and available for academic and non-commercial research purposes as an open-source package at https://github.com/nygenome/lancet. Supplementary data are available at Bioinformatics online.