This is the Linux app named Virmid whose latest release can be downloaded as Virmid-1.2.0.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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Virmid
DESCRIPTION
NEWS:
11-07-2013 A new version Virmid 1.1.0 has been uploaded.
08-29-2013 Virmid paper is now published in Genome Biology.
Kim S et al, "Virmid: accurate detection of somatic mutations with sample impurity inference", Genome Biology 2013, 14:R90
http://genomebiology.com/2013/14/8/R90/abstract
Virmid (Virtual Microdissection for SNP calling) 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). The important features of Virmid are:
•Estimation of accurate proporation of control sample in a (mixed) disease sample
•Improved SNP and somatic mutation calling with regard to the estimated proportion
Features
- Somatic mutation finding
- Sample impurity inference
Audience
Science/Research
Programming Language
Java
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/virmid/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
