VarScan is a tool that detects variants (SNPs and indels) in next-generation sequencing data. The new release (VarScan 2) is implemented in Java, and includes several new features: SAM/BAM compatibility. VarScan now takes SAMtools pileup as input, so it’s compatible with most SAM-friendly short read aligners. For a list of SAM-friendly aligners on which VarScan has been tested, see below. Java implementation, which improves performance and lets VarScan run on any operating system. SNP, indel, and consensus calling. In addition to detecting variants, VarScan calls consensus genotypes based on read counts and allele frequency. Somatic variant detection. Given input from a tumor sample and matched control, VarScan identifies variants and determines their somatic status (Germline, Somatic, or LOH) by comparing the read counts. Exome-based copy number alteration detection. You can also use VarScan 2 to call somatic copy number alterations in tumor sample relative to the matched control. When tumor and normal undergo capture and sequencing with identical protocols, this read depth comparison approach is quite sensitive to detect both focal and large-scale CNAs.