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.

Download or Cite VarScan

Please visit the VarScan Project on for downloads and documentation.

To cite VarScan in your publications, please cite the following:

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, & Wilson RK (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research PMID: 22300766

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics, 25 (17), 2283-5 PMID: 19542151

If you prefer to use only one citation, please cite the Genome Research paper.

VarScan 2 somatic mutation detection

SAM-Friendly Aligners Tested with VarScan

  • BLAT (Roche 454) – the UCSC aligner for long reads, converted from PSL to SAM format
  • Bowtie (Illumina/Solexa) – an ultrafast, memory-efficient short read aligner
  • BWA (Illumina/Solexa, ABI SOLiD) – the Burrows-Wheeler aligner from Heng Li that replaces Maq
  • Maq (Illumina/Solexa, ABI SOLiD) – The widely used Mapping and Alignment with Qualities
  • Novoalign (Illumina/Solexa) – A sensitive short read aligner from Novocraft
  • SSAHA2 (Roche 454) – A fast, SAM-friendly aligner for long reads.
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