pipelines_detect_variants.cwl

Documentation for detect_variants.cwl

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Overview

Detect Variants workflow

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
tumor_bam			File	['.bai', '^.bai']
normal_bam			File	['.bai', '^.bai']
roi_intervals	roi_intervals: regions of interest in which variants will be called	roi_intervals is a list of regions (in interval_list format) within which to call somatic variants	File
strelka_exome_mode			boolean
strelka_cpu_reserved			int?
readcount_minimum_base_quality			int?
readcount_minimum_mapping_quality			int?
scatter_count		scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs	int
varscan_strand_filter			int?
varscan_min_coverage			int?
varscan_min_var_freq			float?
varscan_p_value			float?
varscan_max_normal_freq			float?
pindel_insert_size			int
docm_vcf		Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)	File	['.tbi']
filter_docm_variants		Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls	boolean
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
synonyms_file			File?
annotate_coding_only			boolean?
vep_pick			['null', {'type': 'enum', 'symbols': ['pick', 'flag_pick', 'pick_allele', 'per_gene', 'pick_allele_gene', 'flag_pick_allele', 'flag_pick_allele_gene']}]
vep_plugins			string[]
filter_gnomADe_maximum_population_allele_frequency			float
filter_mapq0_threshold			float
filter_somatic_llr_threshold		Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure.	float
filter_somatic_llr_tumor_purity		Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1	float
filter_somatic_llr_normal_contamination_rate		Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1	float
filter_minimum_depth			int
cle_vcf_filter			boolean
variants_to_table_fields			string[]
variants_to_table_genotype_fields			string[]
vep_to_table_fields			string[]
tumor_sample_name			string
normal_sample_name			string
vep_custom_annotations		custom type, check types directory for input format	../types/vep_custom_annotation.yml#vep_custom_annotation[]
validated_variants		An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF	File?	['.tbi']

Outputs

Name	Label	Description	Type	Secondary Files
mutect_unfiltered_vcf			File	['.tbi']
mutect_filtered_vcf			File	['.tbi']
strelka_unfiltered_vcf			File	['.tbi']
strelka_filtered_vcf			File	['.tbi']
varscan_unfiltered_vcf			File	['.tbi']
varscan_filtered_vcf			File	['.tbi']
pindel_unfiltered_vcf			File	['.tbi']
pindel_filtered_vcf			File	['.tbi']
docm_filtered_vcf			File	['.tbi']
final_vcf			File	['.tbi']
final_filtered_vcf			File	['.tbi']
final_tsv			File
vep_summary			File
tumor_snv_bam_readcount_tsv			File
tumor_indel_bam_readcount_tsv			File
normal_snv_bam_readcount_tsv			File
normal_indel_bam_readcount_tsv			File

Steps

Name	CWL Run
mutect	subworkflows/mutect.cwl
strelka	subworkflows/strelka_and_post_processing.cwl
varscan	subworkflows/varscan_pre_and_post_processing.cwl
pindel	subworkflows/pindel.cwl
docm	subworkflows/docm_cle.cwl
combine	tools/combine_variants.cwl
add_docm_variants	tools/docm_add_variants.cwl
decompose	tools/vt_decompose.cwl
decompose_index	tools/index_vcf.cwl
annotate_variants	tools/vep.cwl
tumor_bam_readcount	tools/bam_readcount.cwl
normal_bam_readcount	tools/bam_readcount.cwl
add_tumor_bam_readcount_to_vcf	subworkflows/vcf_readcount_annotator.cwl
add_normal_bam_readcount_to_vcf	subworkflows/vcf_readcount_annotator.cwl
index	tools/index_vcf.cwl
filter_vcf	subworkflows/filter_vcf.cwl
annotated_filter_bgzip	tools/bgzip.cwl
annotated_filter_index	tools/index_vcf.cwl
variants_to_table	tools/variants_to_table.cwl
add_vep_fields_to_table	tools/add_vep_fields_to_table.cwl