Dataset Information

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

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.

SUBMITTER: Cibulskis K

PROVIDER: S-EPMC3167057 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature

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Publications

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

Cibulskis Kristian K McKenna Aaron A Fennell Tim T Banks Eric E DePristo Mark M Getz Gad G

Bioinformatics (Oxford, England) 20110729 18

<h4>Summary</h4>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.<h4>Availability and implementation</h4>ContEst is a GATK module, and distributed ...[more]

PMID: 21803805

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Dataset Information

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

Summary

Availability and implementation

Contact

Supplementary information

Publications

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

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