Workflow: Detect Variants workflow

Fetched 2023-01-10 06:35:05 GMT
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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)

vep_pick
reference File
tumor_bam File
normal_bam File
vep_plugins String[]
roi_intervals File 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

scatter_count Integer

scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs

synonyms_file File (Optional)
vep_cache_dir Directory
cle_vcf_filter Boolean
varscan_p_value Float (Optional)
tumor_sample_name String
normal_sample_name String
pindel_insert_size Integer
strelka_exome_mode Boolean
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

Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls

filter_minimum_depth Integer
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)
filter_mapq0_threshold Float
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

varscan_max_normal_freq Float (Optional)
variants_to_table_fields String[]
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.

readcount_minimum_base_quality Integer (Optional)
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

readcount_minimum_mapping_quality Integer (Optional)
variants_to_table_genotype_fields String[]
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

filter_gnomADe_maximum_population_allele_frequency Float

Steps

ID Runs Label Doc
docm Detect Docm variants
index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
mutect mutect parallel workflow
pindel pindel parallel workflow
combine
../tools/combine_variants.cwl (CommandLineTool)
CombineVariants (GATK 3.6)
strelka strelka workflow
varscan Varscan Workflow
decompose
../tools/vt_decompose.cwl (CommandLineTool)
run vt decompose
filter_vcf Apply filters to VCF file
decompose_index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
add_docm_variants
../tools/docm_add_variants.cwl (CommandLineTool)
CombineVariants (GATK 3.6)
annotate_variants
../tools/vep.cwl (CommandLineTool)
Ensembl Variant Effect Predictor
variants_to_table
../tools/variants_to_table.cwl (CommandLineTool)
SelectVariants (GATK 4.1.8.1)
tumor_bam_readcount
../tools/bam_readcount.cwl (CommandLineTool)
run bam-readcount
normal_bam_readcount
../tools/bam_readcount.cwl (CommandLineTool)
run bam-readcount
annotated_filter_bgzip
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
annotated_filter_index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
add_vep_fields_to_table
../tools/add_vep_fields_to_table.cwl (CommandLineTool)
add VEP annotation to report
add_tumor_bam_readcount_to_vcf Add snv and indel bam-readcount files to a vcf
add_normal_bam_readcount_to_vcf Add snv and indel bam-readcount files to a vcf

Outputs

ID Type Label Doc
final_tsv File
final_vcf File
vep_summary File
docm_filtered_vcf File
final_filtered_vcf File
mutect_filtered_vcf File
pindel_filtered_vcf File
strelka_filtered_vcf File
varscan_filtered_vcf File
mutect_unfiltered_vcf File
pindel_unfiltered_vcf File
strelka_unfiltered_vcf File
varscan_unfiltered_vcf File
tumor_snv_bam_readcount_tsv File
normal_snv_bam_readcount_tsv File
tumor_indel_bam_readcount_tsv File
normal_indel_bam_readcount_tsv File
Permalink: https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/pipelines/detect_variants.cwl