Virmid is a Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha)
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Genome Biol. 2013 Aug 29;14(8):R90. [Epub ahead of print]
Virmid: accurate detection of somatic mutations with sample impurity inference.
Kim S, Jeong K, Bhutani K, Lee JH, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V.