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Revision: 0:bf8841b0a6b0

Repository 'gvcftools_extract_variants'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/gvcftools_extract_variants

Extract Variants from gVCF files tool metadata

Miscellaneous

Name: Extract Variants from gVCF files

Description: Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.

Id: gvcftools_extract_variants

Guid: toolshed.g2.bx.psu.edu/repos/iuc/gvcftools_extract_variants/gvcftools_extract_variants/0.1

Version: 0.1

Version command string: None

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/iuc/gvcftools_extract_variants/gvcftools_extract_variants/0.1 (this tool)

gvcftools_extract_variants

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

Requirements:

name

version

type

gvcftools

0.17.0

package

Functional tests

name

inputs

outputs

required files

Test-1

gvcf_input: input1.gvcf

vcf_output: variants_output1.vcf

input1.gvcf
variants_output1.vcf

Test-2

advanced|advanced_options_selector: true
gvcf_input: input1.gvcf
advanced|skip_header: True

vcf_output: variants_noheader_output1.vcf

input1.gvcf
variants_noheader_output1.vcf

Test-3

advanced|invert: True
advanced|advanced_options_selector: true
gvcf_input: input1.gvcf

vcf_output: nonvariants_output1.vcf

input1.gvcf
nonvariants_output1.vcf