tools_gatk_haplotype_caller.cwl

Documentation for gatk_haplotype_caller.cwl

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Overview

GATK HaplotypeCaller

Docker Requirement

broadinstitute/gatk:4.1.8.1

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
bam			File	['^.bai']
emit_reference_confidence			{'type': 'enum', 'symbols': ['NONE', 'BP_RESOLUTION', 'GVCF']}
gvcf_gq_bands			{'type': 'array', 'items': 'string', 'inputBinding': {'prefix': '-GQB'}}
intervals			{'type': 'array', 'items': 'string', 'inputBinding': {'prefix': '-L'}}
dbsnp_vcf			File?	['.tbi']
contamination_fraction			string?
max_alternate_alleles		maximum number of alternate alleles to genotype	int?
ploidy		number of chromosomes per sample	int?
read_filter		filters to apply to reads before analysis	string?
output_file_name			string

Outputs

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