tools_select_variants.cwl

Documentation for select_variants.cwl

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Overview

SelectVariants (GATK 4.1.8.1)

Docker Requirement

broadinstitute/gatk:4.1.8.1

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
vcf			File	['.tbi']
interval_list			File?
exclude_filtered			boolean?
output_vcf_basename			string?
samples_to_include		include genotypes from this sample	string[]?
select_type		select only a certain type of variants	['null', {'type': 'enum', 'symbols': ['INDEL', 'SNP', 'MIXED', 'MNP', 'SYMBOLIC', 'NO_VARIATION']}]

Outputs

Name	Label	Description	Type	Secondary Files
filtered_vcf			File	['.tbi']