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Bioinformatics. 2011 Sep 15;27(18):2601-2. doi: 10.1093/bioinformatics/btr446. Epub 2011 Jul 29.

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

Author information

1
Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA. kcibul@broadinstitute.org

Abstract

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 datasets and report their estimated contamination levels.

AVAILABILITY AND IMPLEMENTATION:

ContEst is a GATK 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.

PMID:
21803805
PMCID:
PMC3167057
DOI:
10.1093/bioinformatics/btr446
[Indexed for MEDLINE]
Free PMC Article
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