Method
Virmid: accurate detection of somatic mutations with sample impurity inference
- † Equal contributors
Genome Biology 2013, 14:R90 doi:10.1186/gb-2013-14-8-r90
Published: 29 August 2013Abstract (provisional)
Detection of somatic variation using sequence from disease-control matched datasets 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/.
