1Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health2University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85721, USA3McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA4Department of Medicine5Department of Pathology6Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
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Motivation:Tumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination can generate many spurious calls when sequencing patient-derived xenografts. Paralogous genome sequences can also generate spurious calls when sequencing any tumor. We developed a BLAST-based algorithm, Mouse And Paralog EXterminator (MAPEX), to identify and filter out spurious calls from both these sources.Results:When calling variants from xenografts, MAPEX has similar sensitivity and specificity to more complex algorithms. When applied to any tumor, MAPEX also automatically flags calls that potentially arise from paralogous sequences. Our implementation, mapexr, runs quickly and easily on a desktop computer. MAPEX is thus a useful addition to almost any pipeline for calling genetic variants in tumors.Availability and implementation:The mapexr package for R is available at https://github.com/bmannakee/mapexr under the MIT license.Contact:firstname.lastname@example.org or email@example.com or firstname.lastname@example.orgSupplementary information:Supplementary data are available at Bioinformatics online.