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pipelines_detect_variants.cwl

Travis CI User edited this page Feb 9, 2021 · 25 revisions

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
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