gathered exome alignment and somatic variant detection

Workflow: gathered exome alignment and somatic variant detection

Fetched 2023-01-09 07:18:06 GMT

Verified with cwltool version 3.1.20221201130942

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This workflow is Open Source and may be reused according to the terms of: MIT License

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
docm_vcf	File		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)
omni_vcf	File
vep_pick
reference	File
output_dir	String
somalier_vcf	File
scatter_count	Integer		scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs
synonyms_file	File (Optional)
vep_cache_dir	Directory
bait_intervals	File
bqsr_intervals	String[]
cle_vcf_filter	Boolean
tumor_sequence	https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/sequence_data.yml#sequence_data[]	tumor_sequence: MT sequencing data and readgroup information	tumor_sequence represents the sequencing data for the MT sample as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.
hgvs_annotation	Boolean (Optional)
normal_sequence	https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/sequence_data.yml#sequence_data[]	normal_sequence: WT sequencing data and readgroup information	normal_sequence represents the sequencing data for the WT sample as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.
tumor_cram_name	String (Optional)
varscan_p_value	Float (Optional)
bqsr_known_sites	File[]		One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.
normal_cram_name	String (Optional)
target_intervals	File	target_intervals: interval_list file of targets used in the sequencing experiment	target_intervals is an interval_list corresponding to the targets for the capture reagent. Bed files with this information can be converted to interval_lists with Picard BedToIntervalList. In general for a WES exome reagent bait_intervals and target_intervals are the same.
summary_intervals	https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/labelled_file.yml#labelled_file[]
tumor_sample_name	String
normal_sample_name	String
per_base_intervals	https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/labelled_file.yml#labelled_file[]
pindel_insert_size	Integer
validated_variants	File (Optional)		An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF
vep_ensembl_species	String		ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus
vep_ensembl_version	String		ensembl version - Must be present in the cache directory. Example: 95
vep_to_table_fields	String[]
annotate_coding_only	Boolean (Optional)
filter_docm_variants	Boolean (Optional)		Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls
per_target_intervals	https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/labelled_file.yml#labelled_file[]
strelka_cpu_reserved	Integer (Optional)
varscan_min_coverage	Integer (Optional)
varscan_min_var_freq	Float (Optional)
vep_ensembl_assembly	String		genome assembly to use in vep. Examples: GRCh38 or GRCm38
varscan_strand_filter	Integer (Optional)
vep_custom_annotations	https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[]		custom type, check types directory for input format
qc_minimum_base_quality	Integer (Optional)
target_interval_padding	Integer	target_interval_padding	The effective coverage of capture products generally extends out beyond the actual regions targeted. This parameter allows variants to be called in these wingspan regions, extending this many base pairs from each side of the target regions.
varscan_max_normal_freq	Float (Optional)
variants_to_table_fields	String[]
qc_minimum_mapping_quality	Integer (Optional)
filter_somatic_llr_threshold	Float		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.
mutect_artifact_detection_mode	Boolean
filter_somatic_llr_tumor_purity	Float		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
picard_metric_accumulation_level	String
variants_to_table_genotype_fields	String[]
mutect_max_alt_alleles_in_normal_count	Integer (Optional)
mutect_max_alt_allele_in_normal_fraction	Float (Optional)
filter_somatic_llr_normal_contamination_rate	Float		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

Steps

ID	Runs	Label	Doc
gatherer	../tools/gatherer.cwl (CommandLineTool)
somatic_exome	somatic_exome.cwl (Workflow)	somatic_exome: exome alignment and somatic variant detection	somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml

Outputs

ID	Type	Label	Doc
final_outputs	String[]

Permalink: https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/pipelines/somatic_exome_gathered.cwl