VarScan

Written in Java, VarScan is a command-line utility for identifying simple nucleotide polymorphisms (SNPs) and Indels. It facilitates variant detection for next-generation data parallel sequencing of individual and pooled samples. The tool is free for non-commercial use.

SNPs are DNA sequence variants which usually occur in a population where a single nucleotide in the genome different than the shared sequence varies between the members of biological species or coupled chromosomes. Meanwhile, 'Indel' is a term in molecular biology used to find out when bases are added or removed from DNA.

Based on the data supplied for a single sample, this application detects and filters germline variants by taking into account the read counts, base quality, and allele frequency. Similarly for a tumor-normal pair, it compares the read counts between samples, in order to calculate the somatic status of each germline, somatic or LOH variant. It can merge and intersect two lists of variants.

The usage is java net.sf.varscan.VarScan [COMMAND] [OPTIONS]

The commands available can identify SNPs and Indels from a Sam Tools pileup file (pileup2snp and pileup2indel), along with SNPs and Indels from an mpileup file (mpileup2snp and mpileup2indel), as well as call consensus and variants from a pileup and mpileup file (pileup2cns and mpileup2cns).

Moreover, you can call germline or somatic variants from tumor-normal pileups (somatic), determine the relative tumor copy number from tumor-normal pileups (copynumber), get read counts for a list of variants from a pileup file (readcounts), filter SNPs by coverage, frequency, p-value and other criteria (filter), and filter somatic variants for clusters or Indels (somaticFilter).

Lastly, it's possible to isolate germline, LOH or somatic calls from the output (processSomatic), call copy number changes from the somatic copy number output (copyCaller), compare two lists with positions or variants (compare), as well as restrict the pileup, SNPs or Indels to ROI positions (limit).