Workflow: Detect Variants workflow for WGS pipeline

Fetched 2023-01-04 19:54:35 GMT
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Inputs

ID Type Title Doc
docm_vcf File
vep_pick
reference String
tumor_bam File
normal_bam File
vep_plugins String[] (Optional)
interval_list File
synonyms_file File (Optional)
vep_cache_dir String
cle_vcf_filter Boolean (Optional)
varscan_p_value Float (Optional)
pindel_insert_size Integer
strelka_exome_mode Boolean
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[] (Optional)
annotate_coding_only Boolean (Optional)
filter_docm_variants Boolean (Optional)
filter_minimum_depth Integer (Optional)
mutect_scatter_count Integer (Optional)
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 (Optional)
vep_custom_annotations https://w3id.org/cwl/view/git/3b6d0475c80f5e452793a46a38ee188742b86595/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[] (Optional)
filter_somatic_llr_threshold Float (Optional)
readcount_minimum_base_quality Integer (Optional)
readcount_minimum_mapping_quality Integer (Optional)
variants_to_table_genotype_fields String[] (Optional)
filter_gnomADe_maximum_population_allele_frequency Float (Optional)

Steps

ID Runs Label Doc
docm Detect Docm variants
index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
mutect mutect parallel workflow
combine
../tools/combine_variants_wgs.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 3.6)
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
strelka_filtered_vcf File
varscan_filtered_vcf File
mutect_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/3b6d0475c80f5e452793a46a38ee188742b86595/definitions/pipelines/detect_variants_wgs.cwl