Workflow: Detect Variants workflow

Fetched 2023-01-10 01:27:46 GMT
children parents
workflow cluster_outputs Workflow Outputs cluster_inputs Workflow Inputs reference reference normal_bam_readcount run bam-readcount reference->normal_bam_readcount reference_fasta varscan Varscan Workflow reference->varscan reference combine CombineVariants (GATK 3.6) reference->combine reference tumor_cram_to_bam cram_to_bam workflow reference->tumor_cram_to_bam reference docm Detect Docm variants reference->docm reference tumor_bam_readcount run bam-readcount reference->tumor_bam_readcount reference_fasta normal_cram_to_bam cram_to_bam workflow reference->normal_cram_to_bam reference mutect mutect parallel workflow reference->mutect reference pindel pindel parallel workflow reference->pindel reference variants_to_table SelectVariants (GATK 3.6) reference->variants_to_table reference strelka strelka workflow reference->strelka reference annotate_variants Ensembl Variant Effect Predictor reference->annotate_variants reference strelka_exome_mode strelka_exome_mode strelka_exome_mode->strelka exome_mode normal_cram normal_cram normal_cram->varscan normal_cram normal_cram->docm normal_cram normal_cram->normal_cram_to_bam cram normal_cram->mutect normal_cram normal_cram->pindel normal_cram normal_cram->strelka normal_cram mutect_scatter_count mutect_scatter_count mutect_scatter_count->mutect scatter_count custom_gnomad_vcf custom_gnomad_vcf custom_gnomad_vcf->annotate_variants custom_gnomad_vcf cosmic_vcf cosmic_vcf cosmic_vcf->mutect cosmic_vcf varscan_min_var_freq varscan_min_var_freq varscan_min_var_freq->varscan min_var_freq varscan_strand_filter varscan_strand_filter varscan_strand_filter->varscan strand_filter vep_cache_dir vep_cache_dir vep_cache_dir->annotate_variants cache_dir tumor_cram tumor_cram tumor_cram->varscan tumor_cram tumor_cram->tumor_cram_to_bam cram tumor_cram->docm tumor_cram tumor_cram->mutect tumor_cram tumor_cram->pindel tumor_cram tumor_cram->strelka tumor_cram mutect_max_alt_alleles_in_normal_count mutect_max_alt_alleles_in_normal_count mutect_max_alt_alleles_in_normal_count->mutect max_alt_alleles_in_normal_count dbsnp_vcf dbsnp_vcf dbsnp_vcf->mutect dbsnp_vcf hgvs_annotation hgvs_annotation hgvs_annotation->annotate_variants hgvs variants_to_table_fields variants_to_table_fields variants_to_table_fields->variants_to_table fields panel_of_normals_vcf panel_of_normals_vcf panel_of_normals_vcf->mutect panel_of_normals_vcf pindel_insert_size pindel_insert_size pindel_insert_size->pindel insert_size docm_vcf docm_vcf docm_vcf->docm docm_vcf varscan_min_coverage varscan_min_coverage varscan_min_coverage->varscan min_coverage cle_vcf_filter cle_vcf_filter cle_annotated_vcf_filter cle_annotated_vcf_filter cle_vcf_filter->cle_annotated_vcf_filter filter strelka_cpu_reserved strelka_cpu_reserved strelka_cpu_reserved->strelka cpu_reserved synonyms_file synonyms_file synonyms_file->annotate_variants synonyms_file varscan_max_normal_freq varscan_max_normal_freq varscan_max_normal_freq->varscan max_normal_freq varscan_p_value varscan_p_value varscan_p_value->varscan p_value mutect_artifact_detection_mode mutect_artifact_detection_mode mutect_artifact_detection_mode->mutect artifact_detection_mode coding_only coding_only coding_only->annotate_variants coding_only interval_list interval_list interval_list->varscan interval_list interval_list->docm interval_list interval_list->mutect interval_list interval_list->pindel interval_list interval_list->strelka interval_list vep_to_table_fields vep_to_table_fields add_vep_fields_to_table add VEP annotation to report vep_to_table_fields->add_vep_fields_to_table vep_fields variants_to_table_genotype_fields variants_to_table_genotype_fields variants_to_table_genotype_fields->variants_to_table genotype_fields mutect_max_alt_allele_in_normal_fraction mutect_max_alt_allele_in_normal_fraction mutect_max_alt_allele_in_normal_fraction->mutect max_alt_allele_in_normal_fraction varscan_unfiltered_vcf varscan_unfiltered_vcf normal_bam_readcount_tsv normal_bam_readcount_tsv final_filtered_vcf final_filtered_vcf docm_unfiltered_vcf docm_unfiltered_vcf final_vcf final_vcf docm_filtered_vcf docm_filtered_vcf strelka_filtered_vcf strelka_filtered_vcf strelka_unfiltered_vcf strelka_unfiltered_vcf pindel_filtered_vcf pindel_filtered_vcf final_tsv final_tsv varscan_filtered_vcf varscan_filtered_vcf mutect_unfiltered_vcf mutect_unfiltered_vcf tumor_bam_readcount_tsv tumor_bam_readcount_tsv pindel_unfiltered_vcf pindel_unfiltered_vcf vep_summary vep_summary mutect_filtered_vcf mutect_filtered_vcf annotated_filter_bgzip bgzip VCF cle_annotated_vcf_filter->annotated_filter_bgzip file normal_bam_readcount->normal_bam_readcount_tsv add_normal_bam_readcount_to_vcf add bam_readcount info to vcf normal_bam_readcount->add_normal_bam_readcount_to_vcf bam_readcount_tsv varscan->varscan_unfiltered_vcf varscan->varscan_filtered_vcf varscan->combine varscan_vcf add_tumor_bam_readcount_to_vcf add bam_readcount info to vcf add_tumor_bam_readcount_to_vcf->add_normal_bam_readcount_to_vcf vcf annotated_filter_index vcf index annotated_filter_index->final_filtered_vcf annotated_filter_index->add_vep_fields_to_table vcf annotated_filter_index->variants_to_table vcf combine->normal_bam_readcount vcf combine->tumor_bam_readcount vcf combine->annotate_variants vcf tumor_cram_to_bam->tumor_bam_readcount bam docm->docm_unfiltered_vcf docm->docm_filtered_vcf docm->combine docm_vcf add_vep_fields_to_table->final_tsv tumor_bam_readcount->tumor_bam_readcount_tsv tumor_bam_readcount->add_tumor_bam_readcount_to_vcf bam_readcount_tsv normal_cram_to_bam->normal_bam_readcount bam index vcf index add_normal_bam_readcount_to_vcf->index vcf index->final_vcf index->cle_annotated_vcf_filter annotated_vcf annotated_filter_bgzip->annotated_filter_index vcf mutect->mutect_unfiltered_vcf mutect->mutect_filtered_vcf mutect->combine mutect_vcf pindel->pindel_filtered_vcf pindel->pindel_unfiltered_vcf pindel->combine pindel_vcf variants_to_table->add_vep_fields_to_table tsv strelka->strelka_filtered_vcf strelka->strelka_unfiltered_vcf strelka->combine strelka_vcf annotate_variants->vep_summary annotate_variants->add_tumor_bam_readcount_to_vcf vcf default1 "NORMAL" default1->normal_bam_readcount sample default2 "TUMOR" default2->add_tumor_bam_readcount_to_vcf sample_name default3 "DNA" default3->add_tumor_bam_readcount_to_vcf data_type default4 "TUMOR" default4->tumor_bam_readcount sample default5 "NORMAL" default5->add_normal_bam_readcount_to_vcf sample_name default6 "DNA" default6->add_normal_bam_readcount_to_vcf data_type
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
docm_vcf File
dbsnp_vcf File (Optional)
reference String
cosmic_vcf File (Optional)
tumor_cram File
coding_only Boolean (Optional)
normal_cram File
interval_list File
synonyms_file File (Optional)
vep_cache_dir String (Optional)
cle_vcf_filter Boolean (Optional)
hgvs_annotation Boolean (Optional)
varscan_p_value Float (Optional)
custom_gnomad_vcf File (Optional)
pindel_insert_size Integer
strelka_exome_mode Boolean
vep_to_table_fields String[] (Optional)
mutect_scatter_count Integer (Optional)
panel_of_normals_vcf File (Optional)
strelka_cpu_reserved Integer (Optional)
varscan_min_coverage Integer (Optional)
varscan_min_var_freq Float (Optional)
varscan_strand_filter Integer (Optional)
varscan_max_normal_freq Float (Optional)
variants_to_table_fields String[] (Optional)
mutect_artifact_detection_mode Boolean (Optional)
variants_to_table_genotype_fields String[] (Optional)
mutect_max_alt_alleles_in_normal_count Integer (Optional)
mutect_max_alt_allele_in_normal_fraction Float (Optional)

Steps

ID Runs Label Doc
docm Detect Docm variants
index
index.cwl (CommandLineTool)
vcf index
mutect mutect parallel workflow
pindel pindel parallel workflow
combine
combine_variants.cwl (CommandLineTool)
CombineVariants (GATK 3.6)
strelka strelka workflow
varscan Varscan Workflow
annotate_variants
vep.cwl (CommandLineTool)
Ensembl Variant Effect Predictor
tumor_cram_to_bam cram_to_bam workflow
variants_to_table
variants_to_table.cwl (CommandLineTool)
SelectVariants (GATK 3.6)
normal_cram_to_bam cram_to_bam workflow
tumor_bam_readcount
../pvacseq/bam_readcount.cwl (CommandLineTool)
run bam-readcount
normal_bam_readcount
../pvacseq/bam_readcount.cwl (CommandLineTool)
run bam-readcount
annotated_filter_bgzip
bgzip.cwl (CommandLineTool)
bgzip VCF
annotated_filter_index
index.cwl (CommandLineTool)
vcf index
add_vep_fields_to_table
add_vep_fields_to_table.cwl (CommandLineTool)
add VEP annotation to report
cle_annotated_vcf_filter
cle_annotated_vcf_filter.cwl (CommandLineTool)
cle_annotated_vcf_filter
add_tumor_bam_readcount_to_vcf
add_bam_readcount_to_vcf.cwl (CommandLineTool)
add bam_readcount info to vcf
add_normal_bam_readcount_to_vcf
add_bam_readcount_to_vcf.cwl (CommandLineTool)
add bam_readcount info to vcf

Outputs

ID Type Label Doc
final_tsv File
final_vcf File
vep_summary File
docm_filtered_vcf File
final_filtered_vcf File
docm_unfiltered_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_bam_readcount_tsv File
normal_bam_readcount_tsv File
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/e4c851d65f460e8f48ca184120044fce72cb2433/detect_variants/detect_variants.cwl