VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, IonTorrent, 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:

• Germline variants (SNPs an dindels) in individual samples or pools of samples.
• Shared and private variants in multi-sample datasets (with mpileup).
• Somatic mutations, LOH events, and germline variants in tumor-normal pairs.

• Somatic copy number alterations (CNAs) in tumor-normal exome data

  VarScan is under continued development and improvement at a leading genome center with early access to new sequencing technologies, substantial computing resources, immense public/private datasets, and established expertise in sequencing, genetics, and genomics

  See: http://varscan.sourceforge.net/