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.

Availability and implementation

Lancet is implemented in C++ and available for academic and non-commercial research purposes as an open-source package at

Supplementary information

Supplementary data are available at Bioinformatics online.

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