Monday, August 1, 2011

ContEst: Estimating cross-contamination of human samples in next generation sequencing data

ContEst: Estimating cross-contamination of human samples in next generation sequencing data:

Summary: Here, we present ContEst, a tool for estimating the level of cross-individual contamination in next generation sequencing data. We demonstrate the accuracy of ContEst across a range of contamination levels, sources, and read depths using sequencing data mixed in-silico at known concentrations. We applied our tool to published cancer sequencing data sets and report their estimated contamination levels.

Availability and Implementation: ContEst is a GATK (McKenna, et al., 2010) module, and distributed under a BSD style license at http://www.broadinstitute.org/cancer/cga/contest

Contact:kcibul@broadinstitute.org, gadgetz@broadinstitute.org

Supplementary information: Supplementary data is available at Bioinformatics online


(Via Bioinformatics - Advance Access.)