Workflow: Detect Variants workflow

Fetched 2023-01-09 22:25:07 GMT
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workflow cluster_outputs Workflow Outputs cluster_inputs Workflow Inputs vep_ensembl_version vep_ensembl_version annotate_variants Ensembl Variant Effect Predictor vep_ensembl_version->annotate_variants ensembl_version readcount_minimum_mapping_quality readcount_minimum_mapping_quality tumor_bam_readcount run bam-readcount readcount_minimum_mapping_quality->tumor_bam_readcount min_mapping_quality normal_bam_readcount run bam-readcount readcount_minimum_mapping_quality->normal_bam_readcount min_mapping_quality reference reference variants_to_table SelectVariants (GATK 4.1.8.1) reference->variants_to_table reference reference->tumor_bam_readcount reference_fasta pindel pindel parallel workflow reference->pindel reference strelka strelka workflow reference->strelka reference varscan Varscan Workflow reference->varscan reference mutect mutect parallel workflow reference->mutect reference reference->normal_bam_readcount reference_fasta combine CombineVariants (GATK 3.6) reference->combine reference reference->annotate_variants reference filter_vcf Apply filters to VCF file reference->filter_vcf reference roi_intervals roi_intervals: regions of interest in which variants will be called roi_intervals->pindel interval_list roi_intervals->strelka interval_list roi_intervals->varscan interval_list roi_intervals->mutect interval_list varscan_min_var_freq varscan_min_var_freq varscan_min_var_freq->varscan min_var_freq readcount_minimum_base_quality readcount_minimum_base_quality readcount_minimum_base_quality->tumor_bam_readcount min_base_quality readcount_minimum_base_quality->normal_bam_readcount min_base_quality normal_bam normal_bam normal_bam->pindel normal_bam normal_bam->strelka normal_bam normal_bam->varscan normal_bam normal_bam->mutect normal_bam normal_bam->normal_bam_readcount bam tumor_bam tumor_bam tumor_bam->tumor_bam_readcount bam tumor_bam->pindel tumor_bam tumor_bam->strelka tumor_bam tumor_bam->varscan tumor_bam tumor_bam->mutect tumor_bam tumor_bam->filter_vcf tumor_bam tumor_sample_name tumor_sample_name tumor_sample_name->tumor_bam_readcount sample tumor_sample_name->pindel tumor_sample_name tumor_sample_name->strelka tumor_sample_name tumor_sample_name->varscan tumor_sample_name tumor_sample_name->mutect tumor_sample_name add_tumor_bam_readcount_to_vcf Add snv and indel bam-readcount files to a vcf tumor_sample_name->add_tumor_bam_readcount_to_vcf sample_name tumor_sample_name->filter_vcf tumor_sample_name vep_plugins vep_plugins vep_plugins->annotate_variants plugins variants_to_table_fields variants_to_table_fields variants_to_table_fields->variants_to_table fields filter_minimum_depth filter_minimum_depth filter_minimum_depth->filter_vcf filter_minimum_depth vep_ensembl_assembly vep_ensembl_assembly vep_ensembl_assembly->annotate_variants ensembl_assembly synonyms_file synonyms_file synonyms_file->annotate_variants synonyms_file filter_mapq0_threshold filter_mapq0_threshold filter_mapq0_threshold->filter_vcf filter_mapq0_threshold varscan_strand_filter varscan_strand_filter varscan_strand_filter->varscan strand_filter pindel_insert_size pindel_insert_size pindel_insert_size->pindel insert_size normal_sample_name normal_sample_name add_normal_bam_readcount_to_vcf Add snv and indel bam-readcount files to a vcf normal_sample_name->add_normal_bam_readcount_to_vcf sample_name normal_sample_name->pindel normal_sample_name normal_sample_name->strelka normal_sample_name normal_sample_name->varscan normal_sample_name normal_sample_name->normal_bam_readcount sample normal_sample_name->filter_vcf normal_sample_name filter_somatic_llr_normal_contamination_rate filter_somatic_llr_normal_contamination_rate filter_somatic_llr_normal_contamination_rate->filter_vcf filter_somatic_llr_normal_contamination_rate strelka_cpu_reserved strelka_cpu_reserved strelka_cpu_reserved->strelka cpu_reserved cle_vcf_filter cle_vcf_filter cle_vcf_filter->filter_vcf do_cle_vcf_filter filter_somatic_llr_threshold filter_somatic_llr_threshold filter_somatic_llr_threshold->filter_vcf filter_somatic_llr_threshold vep_ensembl_species vep_ensembl_species vep_ensembl_species->annotate_variants ensembl_species variants_to_table_genotype_fields variants_to_table_genotype_fields variants_to_table_genotype_fields->variants_to_table genotype_fields vep_pick vep_pick vep_pick->annotate_variants pick varscan_p_value varscan_p_value varscan_p_value->varscan p_value vep_cache_dir vep_cache_dir vep_cache_dir->annotate_variants cache_dir annotate_coding_only annotate_coding_only annotate_coding_only->annotate_variants coding_only varscan_min_coverage varscan_min_coverage varscan_min_coverage->varscan min_coverage varscan_max_normal_freq varscan_max_normal_freq varscan_max_normal_freq->varscan max_normal_freq filter_somatic_llr_tumor_purity filter_somatic_llr_tumor_purity filter_somatic_llr_tumor_purity->filter_vcf filter_somatic_llr_tumor_purity 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 strelka_exome_mode strelka_exome_mode strelka_exome_mode->strelka exome_mode scatter_count scatter_count scatter_count->pindel scatter_count scatter_count->varscan scatter_count scatter_count->mutect scatter_count final_tsv final_tsv normal_indel_bam_readcount_tsv normal_indel_bam_readcount_tsv tumor_indel_bam_readcount_tsv tumor_indel_bam_readcount_tsv tumor_snv_bam_readcount_tsv tumor_snv_bam_readcount_tsv pindel_unfiltered_vcf pindel_unfiltered_vcf varscan_unfiltered_vcf varscan_unfiltered_vcf final_filtered_vcf final_filtered_vcf final_vcf final_vcf strelka_unfiltered_vcf strelka_unfiltered_vcf pindel_filtered_vcf pindel_filtered_vcf mutect_unfiltered_vcf mutect_unfiltered_vcf normal_snv_bam_readcount_tsv normal_snv_bam_readcount_tsv mutect_filtered_vcf mutect_filtered_vcf vep_summary vep_summary strelka_filtered_vcf strelka_filtered_vcf varscan_filtered_vcf varscan_filtered_vcf variants_to_table->add_vep_fields_to_table tsv index vcf index add_normal_bam_readcount_to_vcf->index vcf index->final_vcf index->filter_vcf vcf tumor_bam_readcount->tumor_indel_bam_readcount_tsv tumor_bam_readcount->tumor_snv_bam_readcount_tsv tumor_bam_readcount->add_tumor_bam_readcount_to_vcf snv_bam_readcount_tsv tumor_bam_readcount->add_tumor_bam_readcount_to_vcf indel_bam_readcount_tsv pindel->pindel_unfiltered_vcf pindel->pindel_filtered_vcf pindel->combine pindel_vcf annotated_filter_bgzip bgzip VCF annotated_filter_index vcf index annotated_filter_bgzip->annotated_filter_index vcf add_vep_fields_to_table->final_tsv decompose run vt decompose decompose_index vcf index decompose->decompose_index vcf strelka->strelka_unfiltered_vcf strelka->strelka_filtered_vcf strelka->combine strelka_vcf annotated_filter_index->final_filtered_vcf annotated_filter_index->variants_to_table vcf annotated_filter_index->add_vep_fields_to_table vcf decompose_index->annotate_variants vcf varscan->varscan_unfiltered_vcf varscan->varscan_filtered_vcf varscan->combine varscan_vcf mutect->mutect_unfiltered_vcf mutect->mutect_filtered_vcf mutect->combine mutect_vcf normal_bam_readcount->normal_indel_bam_readcount_tsv normal_bam_readcount->normal_snv_bam_readcount_tsv normal_bam_readcount->add_normal_bam_readcount_to_vcf snv_bam_readcount_tsv normal_bam_readcount->add_normal_bam_readcount_to_vcf indel_bam_readcount_tsv combine->decompose vcf annotate_variants->vep_summary annotate_variants->tumor_bam_readcount vcf annotate_variants->normal_bam_readcount vcf annotate_variants->add_tumor_bam_readcount_to_vcf vcf add_tumor_bam_readcount_to_vcf->add_normal_bam_readcount_to_vcf vcf filter_vcf->annotated_filter_bgzip file default1 "DNA" default1->add_normal_bam_readcount_to_vcf data_type default2 "DNA" default2->add_tumor_bam_readcount_to_vcf data_type
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Inputs

ID Type Title Doc
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
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_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
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

Steps

ID Runs Label Doc
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
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
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/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/pipelines/detect_variants_nonhuman.cwl