pdxBlacklist: Identifying artefactual variants in patient-derived xenograft samples

Abstract

Patient-derived tumor xenograft (PDX) samples typically represent a mixture of mouse and human tissue. Variant call sets derived from sequencing such samples are commonly contaminated with false positive variants that arise when mouse-derived reads are mapped to the human genome. pdxBlacklist is a novel approach designed to rapidly identify these false-positive variants, and thus significantly improve variant call set quality.\n\nAvailabilitypdxBlacklist is freely available on GitHub: https://github.com/MaxSalm/pdxBlacklist\n\nContactmaxsalm3@gmail.com\n\nSupplementary informationSupplementary data are available.