A platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation: 1) germline variants (SNPs and indels) in individual samples or pools of samples, 2) multi-sample variants (shared or private) in multi-sample datasets (with mpileup), 3) somatic mutations, LOH events, and germline variants in tumor-normal pairs and 4) somatic copy number alterations (CNAs) in tumor-normal exome data.
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(Stead et al., 2013) Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution. Human mutation.
(Roberts et al., 2013) A comparative analysis of algorithms for somatic SNV detection in cancer. Bioinformatics.
(Wang et al., 2013) Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome medicine.