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VarScan mpileup (version 2.4.3.1)

Samtools pileup dataset:

Analysis type:

Minimum coverage:

Minimum depth at a position to make a call

Minimum supporting reads:

Minimum number (default: 2) of variant-supporting reads at a position required to make a call

Minimum base quality:

The minimum base quality at the variant position required to use a read for calling

Minimum variant allele frequency:

Minimum variant allele frequency (default: 0.01) required for calling a variant

Minimum homozygous variant allele frequency:

Minimum variant allele frequency (default: 0.75) required for calling a homozygous genotype

Default p-value threshold for calling variants:

Ignore variants with >90% support on one strand:

sample_names:

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.

Input

mpileup file - The SAMtools mpileup file

Output

VarScan produces a VCF 4.1 dataset as output.