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VarScan - Variant detection in massively parallel sequencing data

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequencyh. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.

Installation

VarScan is implemented in Java, so it runs on any machine with the Java Virtual Machine (VM) installed. Most operating systems (Linux, Mac OSX, Windows) come with Java pre-installed. The steps to install and run VarScan:

1. Download the latest VarScan JAR file
2. Run VarScan with the command

java -jar VarScan.v2.2.jar

Running the above command with no arguments will display VarScan usage.

Usage

Like SAMtools, all VarScan tools are accessed by subcommands:

USAGE: java java -jar VarScan.v2.2.jar [COMMAND] [OPTIONS] 

COMMANDS:
        pileup2snp [pileup_file] >outfile.snp           Call SNPs from a pileup file
        pileup2indel [pileup_file] >outfile.indel       Call indels a pileup file
        pileup2cns [pileup_file] >outfile.cns           Call consensus and variants from a pileup file

        somatic [normal_pileup] [tumor_pileup] varscan.out Call germline/somatic variants from tumor-normal data

        readcounts [pileup] --variants-file [variants]  Compute read counts supporting each allele

        filter [outfile.snp] >outfile.snp.filter                Filter SNPs/indels by coverage, frequency, p-value.
        somaticFilter varscan.out.snp >varscan.out.snp.filter   Filter somatic variants for clusters/indels

        compare [file1] [file2] [type] [output]         Merge/intersect/substract 2 sets of variants
        limit [infile] [--positions-file] [--regions-file] Restrict pileup/snps/indels to ROI positions