Loading Toolbox...

VarScan mpileup

for variant detection (Galaxy Version 2.4.3.1)

Tool Parameters

Please provide a value for this option.

Samtools pileup dataset * required

No datasets with pileup elements available

Analysis type *

Minimum coverage *

Minimum depth at a position to make a call (--min-coverage)

Minimum supporting reads *

Minimum number (default: 2) of variant-supporting reads at a position required to make a call (--min-reads2)

Minimum base quality *

The minimum base quality at the variant position required to use a read for calling (--min-avg-qual)

Minimum variant allele frequency *

Minimum variant allele frequency (default: 0.01) required for calling a variant (--min-var-freq)

Minimum homozygous variant allele frequency *

Minimum variant allele frequency (default: 0.75) required for calling a homozygous genotype (--min-freq-for-hom)

Default p-value threshold for calling variants *

(--p-value)

Ignore variants with >90% support on one strand *

sample_names - optional

Separate sample names by comma; leave blank to use default sample names.

Additional Options

Email notification

Send an email notification when the job completes.

Help

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.

Help Forum

There are no questions on the Help Forum about this tool.

Ask a new question

Unnamed history

Loading History...

Draggable