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VarScan mpileup (version
Minimum depth at a position to make a call
Minimum number (default: 2) of variant-supporting reads at a position required to make a call
The minimum base quality at the variant position required to use a read for calling
Minimum variant allele frequency (default: 0.01) required for calling a variant
Minimum variant allele frequency (default: 0.75) required for calling a homozygous genotype
Separate sample names by comma; leave blank to use default sample names.

VarScan Overview

VarScan performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. Full documentation of the command line package is available here.


mpileup file - The SAMtools mpileup file


VarScan produces a VCF 4.1 dataset as output.