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Genome Biol. 2013 Aug 29;14(8):R90. doi: 10.1186/gb-2013-14-8-r90.

Virmid: accurate detection of somatic mutations with sample impurity inference.

Abstract

Detection of somatic variation using sequence from disease-control matched data sets is a critical first step. In many cases including cancer, however, it is hard to isolate pure disease tissue, and the impurity hinders accurate mutation analysis by disrupting overall allele frequencies. Here, we propose a new method, Virmid, that explicitly determines the level of impurity in the sample, and uses it for improved detection of somatic variation. Extensive tests on simulated and real sequencing data from breast cancer and hemimegalencephaly demonstrate the power of our model. A software implementation of our method is available at http://sourceforge.net/projects/virmid/.

PMID:
23987214
[PubMed - in process]
PMCID:
PMC4054681
Free PMC Article

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