Summary
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.
Availability: pdxBlacklist is freely available on GitHub: https://github.com/MaxSalm/pdxBlacklist
Contact: maxsalm3{at}gmail.com
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.