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Revision: 1:9a39c4105901

Repository 'varscan_mpileup2snp_from_bam'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/yhoogstrate/varscan_mpileup2snp_from_bam

VarScan2 Call SNPs from BAM tool metadata

Miscellaneous

Name: VarScan2 Call SNPs from BAM

Description: VarScan2 SNP/SNV detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.

Id: varscan_mpileup2snp_from_bam

Guid: toolshed.g2.bx.psu.edu/repos/yhoogstrate/varscan_mpileup2snp_from_bam/varscan_mpileup2snp_from_bam/2.4.2.a

Version: 2.4.2.a

Version command string: varscan 2>&1 | head -n 1

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/yhoogstrate/varscan_mpileup2snp_from_bam/varscan_mpileup2snp_from_bam/2.4.2.a (this tool)

toolshed.g2.bx.psu.edu/repos/yhoogstrate/varscan_mpileup2snp_from_bam/varscan_mpileup2snp_from_bam/2.3.6.a

varscan_mpileup2snp_from_bam

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

varscan

2.4.2

package

sambamba

0.6.5

package

Functional tests

name

inputs

outputs

required files

Test-1

reference_genome_source|reference_genome: example.fa
reference_genome_source|source_select: history
alignments: example.bam
extended_parameters_regions|sambamba_regions: entire_genome
extended_parameters|parameters: default

snv_output: example.vcf

example.bam
example.fa
example.vcf