VarScan
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.
Download or Cite VarScan
Please visit the VarScan Project on Sourceforge.net for downloads and documentation.
To cite VarScan in your publications, please use this reference:
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
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.
