Galaxy |

Repository revision

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 a mpileup file tool metadata

Miscellaneous

Name: VarScan2 Call SNPs from a mpileup file

Description: VarScan2 SNP/SNV detection; directly from a *.mpileup file.

Id: varscan_mpileup2snp

Guid: toolshed.g2.bx.psu.edu/repos/yhoogstrate/varscan_mpileup2snp_from_bam/varscan_mpileup2snp/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/2.4.2.a (this tool)

toolshed.g2.bx.psu.edu/repos/yhoogstrate/varscan_mpileup2snp_from_bam/varscan_mpileup2snp/2.3.6.a

varscan_mpileup2snp

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

Requirements:

name

version

type

varscan

2.4.2

package

Functional tests

name

inputs

outputs

required files

Test-1

extended_parameters|parameters: default
mpileup_input: hg19_mutant.mpileup

snv_output: hg19_mutant.vcf

hg19_mutant.mpileup
hg19_mutant.vcf

Test-2

extended_parameters|varscan_min_avg_qual: 15
extended_parameters|varscan_min_freq_for_hom: 0.75
extended_parameters|varscan_min_var_freq: 0.01
extended_parameters|varscan_min_reads2: 2
extended_parameters|varscan_variants: False
extended_parameters|parameters: extended
mpileup_input: hg19_mutant.mpileup
extended_parameters|varscan_strand_filter: True
extended_parameters|varscan_min_coverage: 8
extended_parameters|varscan_p_value: 0.99

snv_output: hg19_mutant.2.vcf

hg19_mutant.mpileup
hg19_mutant.2.vcf