subworkflows_joint_genotype.cwl

Documentation for joint_genotype.cwl

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joint genotyping for trios or small cohorts

Name	Description	Type	Secondary Files
reference		['string', 'File']	['.fai', '^.dict']
gvcfs		File[]
intervals	intervals used to parallelize genotyping. Example: chr1],[chr2],[chr3],[chr4,chr5	{'type': 'array', 'items': {'type': 'array', 'items': 'string'}}
vep_cache_dir		['string', 'Directory']
vep_ensembl_assembly	genome assembly to use in vep. Examples: GRCh38 or GRCm38	string
vep_ensembl_version	ensembl version - Must be present in the cache directory. Example: 95	string
vep_ensembl_species	ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus	string
vep_plugins		string[]
synonyms_file		File?
annotate_coding_only		boolean?
vep_custom_annotations	custom type, check types directory for input format	../types/vep_custom_annotation.yml#vep_custom_annotation[]
roi_intervals	region of interest interval list file, used to limit called variants in final filtered output files	File
variants_to_table_fields		string[]?
variants_to_table_genotype_fields		string[]?
vep_to_table_fields		string[]?
final_tsv_prefix		string?
filter_gnomAD_maximum_population_allele_frequency		float

Name	Type	Secondary Files
raw_vcf	File	['.tbi']
final_vcf	File	['.tbi']
filtered_vcf	File	['.tbi']
vep_summary	File
final_tsv	File
filtered_tsv	File

Name	CWL Run
combine_gvcfs	tools/combine_gvcfs.cwl
genotype_gvcf	tools/gatk_genotypegvcfs.cwl
merge_vcfs	tools/picard_merge_vcfs.cwl
annotate_variants	tools/vep.cwl
bgzip_index_annotated_vcf	subworkflows/bgzip_and_index.cwl
filter_vcf	subworkflows/germline_filter_vcf.cwl
filtered_variants_to_table	tools/variants_to_table.cwl
filtered_add_vep_fields_to_table	tools/add_vep_fields_to_table.cwl
set_filtered_tsv_name	tools/staged_rename.cwl
final_variants_to_table	tools/variants_to_table.cwl
final_add_vep_fields_to_table	tools/add_vep_fields_to_table.cwl
set_final_tsv_name	tools/staged_rename.cwl