pipelines_somatic_wgs.cwl

Documentation for somatic_wgs.cwl

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Overview

Whole genome alignment and somatic variant detection

Inputs

Name	Label	Description	Type	Secondary Files
reference			string
tumor_sequence	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.	../types/sequence_data.yml#sequence_data[]
tumor_name			string?
normal_sequence	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.	../types/sequence_data.yml#sequence_data[]
normal_name			string?
trimming			['../types/trimming_options.yml#trimming_options', 'null']
bqsr_known_sites		One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.	File[]	['.tbi']
bqsr_intervals			string[]
target_intervals			File
per_base_intervals			../types/labelled_file.yml#labelled_file[]
per_target_intervals			../types/labelled_file.yml#labelled_file[]
qc_intervals			File
summary_intervals			../types/labelled_file.yml#labelled_file[]
omni_vcf			File	['.tbi']
picard_metric_accumulation_level			string
qc_minimum_mapping_quality			int?
qc_minimum_base_quality			int?
strelka_cpu_reserved			int?
scatter_count		scatters each supported variant detector (varscan, mutect) into this many parallel jobs	int
mutect_artifact_detection_mode			boolean
mutect_max_alt_allele_in_normal_fraction			float?
mutect_max_alt_alleles_in_normal_count			int?
varscan_strand_filter			int?
varscan_min_coverage			int?
varscan_min_var_freq			float?
varscan_p_value			float?
varscan_max_normal_freq			float?
docm_vcf			File	['.tbi']
filter_docm_variants			boolean?
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
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']}]
cle_vcf_filter			boolean
variants_to_table_fields			string[]
variants_to_table_genotype_fields			string[]
vep_to_table_fields			string[]
vep_custom_annotations		custom type, check types directory for input format	../types/vep_custom_annotation.yml#vep_custom_annotation[]
manta_call_regions			File?	['.tbi']
manta_non_wgs			boolean?
manta_output_contigs			boolean?
somalier_vcf			File
tumor_sample_name			string
normal_sample_name			string
validated_variants		An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF	File?	['.tbi']
cnvkit_target_average_size		approximate size of split target bins for CNVkit; if not set a suitable window size will be set by CNVkit automatically	int?

Outputs

Name	Label	Description	Type	Secondary Files
tumor_cram			File
tumor_mark_duplicates_metrics			File
tumor_insert_size_metrics			File
tumor_alignment_summary_metrics			File
tumor_per_target_coverage_metrics			File[]
tumor_per_target_hs_metrics			File[]
tumor_per_base_coverage_metrics			File[]
tumor_per_base_hs_metrics			File[]
tumor_summary_hs_metrics			File[]
tumor_flagstats			File
tumor_verify_bam_id_metrics			File
tumor_verify_bam_id_depth			File
tumor_insert_size_histogram			File
tumor_gc_bias_metrics			File
tumor_gc_bias_metrics_chart			File
tumor_gc_bias_metrics_summary			File
tumor_wgs_metrics			File
normal_cram			File
normal_mark_duplicates_metrics			File
normal_insert_size_metrics			File
normal_alignment_summary_metrics			File
normal_per_target_coverage_metrics			File[]
normal_per_target_hs_metrics			File[]
normal_per_base_coverage_metrics			File[]
normal_per_base_hs_metrics			File[]
normal_summary_hs_metrics			File[]
normal_flagstats			File
normal_verify_bam_id_metrics			File
normal_verify_bam_id_depth			File
normal_insert_size_histogram			File
normal_gc_bias_metrics			File
normal_gc_bias_metrics_chart			File
normal_gc_bias_metrics_summary			File
normal_wgs_metrics			File
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']
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
diploid_variants			File?	['.tbi']
somatic_variants			File?	['.tbi']
all_candidates			File	['.tbi']
small_candidates			File	['.tbi']
tumor_only_variants			File?	['.tbi']
somalier_concordance_metrics			File
somalier_concordance_statistics			File

Steps

Name	CWL Run
tumor_alignment_and_qc	pipelines/alignment_wgs.cwl
normal_alignment_and_qc	pipelines/alignment_wgs.cwl
concordance	tools/concordance.cwl
detect_variants	pipelines/detect_variants_wgs.cwl
cnvkit	tools/cnvkit_batch.cwl
manta	tools/manta_somatic.cwl
tumor_bam_to_cram	tools/bam_to_cram.cwl
tumor_index_cram	tools/index_cram.cwl
normal_bam_to_cram	tools/bam_to_cram.cwl
normal_index_cram	tools/index_cram.cwl