VarScan performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1
java -jar VarScan.jar [COMMAND] [OPTIONS]
analysis type
single nucleotide detection Identify SNPs from an mpileup file
insertions and deletion Identify indels an mpileup file
consensus genotype Call consensus and variants from an mpileup file
min-coverage
Minimum read depth at a position to make a call [8]
min-reads2
Minimum supporting reads at a position to call variants [2]
min-avg-qual
Minimum base quality at a position to count a read [15]
min-var-freq
Minimum variant allele frequency threshold [0.01]
min-freq-for-hom
Minimum frequency to call homozygote [0.75]
p-value
Default p-value threshold for calling variants [99e-02]
strand-filter
Ignore variants with >90% support on one strand [1]
output-vcf
If set to 1, outputs in VCF format
vcf-sample-list
For VCF output, a list of sample names in order, one per line
variants
Report only variant (SNP/indel) positions [0]