pipelines_germline_exome.cwl

Documentation for germline_exome.cwl

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Overview

exome alignment and germline variant detection

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa']
sequence	sequence: sequencing data and readgroup information	sequence represents the sequencing data 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[]
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[]?
bait_intervals	bait_intervals: interval_list file of baits used in the sequencing experiment	bait_intervals is an interval_list corresponding to the baits used in sequencing reagent. These are essentially coordinates for regions you were able to design probes for in the reagent. Typically the reagent provider has this information available in bed format and it can be converted to an interval_list with Picard BedToIntervalList. Astrazeneca also maintains a repo of baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data	File
target_intervals	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.	File
target_interval_padding	target_interval_padding: number of bp flanking each target region in which to allow variant calls	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.	int
per_base_intervals			../types/labelled_file.yml#labelled_file[]
per_target_intervals			../types/labelled_file.yml#labelled_file[]
summary_intervals			../types/labelled_file.yml#labelled_file[]
omni_vcf			File	['.tbi']
picard_metric_accumulation_level			string
gvcf_gq_bands			string[]
intervals			{'type': 'array', 'items': {'type': 'array', 'items': 'string'}}
ploidy			int?
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		array of plugins to use when running vep	string[]?
synonyms_file			File?
annotate_coding_only			boolean?
qc_minimum_mapping_quality			int?
qc_minimum_base_quality			int?
vep_custom_annotations		custom type, check types directory for input format	../types/vep_custom_annotation.yml#vep_custom_annotation[]
variants_to_table_fields			string[]?
variants_to_table_genotype_fields			string[]?
vep_to_table_fields			string[]?

Outputs

Name	Label	Description	Type	Secondary Files
cram			File
mark_duplicates_metrics			File
insert_size_metrics			File
insert_size_histogram			File
alignment_summary_metrics			File
hs_metrics			File
per_target_coverage_metrics			File[]
per_target_hs_metrics			File[]
per_base_coverage_metrics			File[]
per_base_hs_metrics			File[]
summary_hs_metrics			File[]
flagstats			File
verify_bam_id_metrics			File
verify_bam_id_depth			File
raw_vcf			File	['.tbi']
final_vcf			File	['.tbi']
filtered_vcf			File	['.tbi']
vep_summary			File
final_tsv			File
filtered_tsv			File

Steps

Name	CWL Run
alignment_and_qc	pipelines/alignment_exome.cwl
extract_freemix
pad_target_intervals	tools/interval_list_expand.cwl
detect_variants	subworkflows/germline_detect_variants.cwl
bam_to_cram	tools/bam_to_cram.cwl
index_cram	tools/index_cram.cwl