Workflow: wgs alignment and germline variant detection

Fetched 2023-01-09 22:52:21 GMT
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workflow cluster_outputs Workflow Outputs cluster_inputs Workflow Inputs cnvkit_drop_low_coverage cnvkit_drop_low_coverage sv_detect_variants Subworkflow to allow calling different SV callers which require bam files as inputs cnvkit_drop_low_coverage->sv_detect_variants cnvkit_drop_low_coverage sv_filter_paired_count sv_filter_paired_count sv_filter_paired_count->sv_detect_variants sv_paired_count annotate_coding_only annotate_coding_only detect_variants exome alignment and germline variant detection annotate_coding_only->detect_variants annotate_coding_only synonyms_file synonyms_file synonyms_file->detect_variants synonyms_file cnvkit_reference_cnn cnvkit_reference_cnn cnvkit_reference_cnn->sv_detect_variants cnvkit_reference_cnn ploidy ploidy ploidy->detect_variants ploidy minimum_base_quality minimum_base_quality alignment_and_qc wgs alignment with qc minimum_base_quality->alignment_and_qc minimum_base_quality sv_filter_alt_abundance_percentage sv_filter_alt_abundance_percentage sv_filter_alt_abundance_percentage->sv_detect_variants sv_alt_abundance_percentage variant_reporting_intervals variant_reporting_intervals variant_reporting_intervals->detect_variants limit_variant_intervals disclaimer_text disclaimer_text add_disclaimer_filtered_tsv Insert an arbitrary string at a specific line of a file disclaimer_text->add_disclaimer_filtered_tsv some_text add_disclaimer_final_vcf Insert an arbitrary string at a specific line of a gzipped file disclaimer_text->add_disclaimer_final_vcf some_text add_disclaimer_survivor_sv_tsv Insert an arbitrary string at a specific line of a file disclaimer_text->add_disclaimer_survivor_sv_tsv some_text add_disclaimer_bcftools_sv_tsv Insert an arbitrary string at a specific line of a file disclaimer_text->add_disclaimer_bcftools_sv_tsv some_text add_disclaimer_bcftools_filtered_sv_tsv Insert an arbitrary string at a specific line of a file disclaimer_text->add_disclaimer_bcftools_filtered_sv_tsv some_text add_disclaimer_filtered_vcf Insert an arbitrary string at a specific line of a gzipped file disclaimer_text->add_disclaimer_filtered_vcf some_text add_disclaimer_survivor_sv_vcf Insert an arbitrary string at a specific line of a gzipped file disclaimer_text->add_disclaimer_survivor_sv_vcf some_text add_disclaimer_final_tsv Insert an arbitrary string at a specific line of a file disclaimer_text->add_disclaimer_final_tsv some_text add_disclaimer_bcftools_sv_vcf Insert an arbitrary string at a specific line of a gzipped file disclaimer_text->add_disclaimer_bcftools_sv_vcf some_text merge_same_type merge_same_type merge_same_type->sv_detect_variants merge_same_type vep_to_table_fields vep_to_table_fields vep_to_table_fields->detect_variants vep_to_table_fields trimming trimming trimming->alignment_and_qc trimming cnvkit_male_reference cnvkit_male_reference cnvkit_male_reference->sv_detect_variants cnvkit_male_reference smoove_exclude_regions smoove_exclude_regions smoove_exclude_regions->sv_detect_variants smoove_exclude_regions reference reference reference->detect_variants reference reference->alignment_and_qc reference bam_to_cram BAM to CRAM conversion reference->bam_to_cram reference reference->sv_detect_variants reference vep_cache_dir vep_cache_dir vep_cache_dir->detect_variants vep_cache_dir merge_min_svs merge_min_svs merge_min_svs->sv_detect_variants merge_min_svs cnv_filter_duplication_depth cnv_filter_duplication_depth cnv_filter_duplication_depth->sv_detect_variants cnv_duplication_depth cnvkit_diagram cnvkit_diagram cnvkit_diagram->sv_detect_variants cnvkit_diagram gvcf_gq_bands gvcf_gq_bands gvcf_gq_bands->detect_variants gvcf_gq_bands vep_ensembl_assembly vep_ensembl_assembly vep_ensembl_assembly->detect_variants vep_ensembl_assembly vep_ensembl_assembly->sv_detect_variants genome_build qc_intervals qc_intervals qc_intervals->alignment_and_qc intervals manta_output_contigs manta_output_contigs manta_output_contigs->sv_detect_variants manta_output_contigs vep_ensembl_version vep_ensembl_version vep_ensembl_version->detect_variants vep_ensembl_version per_base_intervals per_base_intervals per_base_intervals->alignment_and_qc per_base_intervals cnvkit_vcf_name cnvkit_vcf_name cnvkit_vcf_name->sv_detect_variants cnvkit_vcf_name cnv_filter_deletion_depth cnv_filter_deletion_depth cnv_filter_deletion_depth->sv_detect_variants cnv_deletion_depth cnvkit_method cnvkit_method cnvkit_method->sv_detect_variants cnvkit_method merge_estimate_sv_distance merge_estimate_sv_distance merge_estimate_sv_distance->sv_detect_variants merge_estimate_sv_distance merge_same_strand merge_same_strand merge_same_strand->sv_detect_variants merge_same_strand sv_filter_split_count sv_filter_split_count sv_filter_split_count->sv_detect_variants sv_split_count manta_call_regions manta_call_regions manta_call_regions->sv_detect_variants manta_call_regions vep_plugins vep_plugins vep_plugins->detect_variants vep_plugins summary_intervals summary_intervals summary_intervals->alignment_and_qc summary_intervals vep_custom_annotations vep_custom_annotations vep_custom_annotations->detect_variants vep_custom_annotations sequence sequence: sequencing data and readgroup information sequence->alignment_and_qc sequence bqsr_known_sites bqsr_known_sites bqsr_known_sites->alignment_and_qc bqsr_known_sites variants_to_table_fields variants_to_table_fields variants_to_table_fields->detect_variants variants_to_table_fields intervals intervals intervals->detect_variants intervals vep_ensembl_species vep_ensembl_species vep_ensembl_species->detect_variants vep_ensembl_species minimum_mapping_quality minimum_mapping_quality minimum_mapping_quality->alignment_and_qc minimum_mapping_quality per_target_intervals per_target_intervals per_target_intervals->alignment_and_qc per_target_intervals manta_non_wgs manta_non_wgs manta_non_wgs->sv_detect_variants manta_non_wgs variants_to_table_genotype_fields variants_to_table_genotype_fields variants_to_table_genotype_fields->detect_variants variants_to_table_genotype_fields merge_max_distance merge_max_distance merge_max_distance->sv_detect_variants merge_max_distance blocklist_bedpe blocklist_bedpe blocklist_bedpe->sv_detect_variants blocklist_bedpe omni_vcf omni_vcf omni_vcf->alignment_and_qc omni_vcf cnv_filter_min_size cnv_filter_min_size cnv_filter_min_size->sv_detect_variants cnv_filter_min_size bqsr_intervals bqsr_intervals bqsr_intervals->alignment_and_qc bqsr_intervals cnvkit_scatter_plot cnvkit_scatter_plot cnvkit_scatter_plot->sv_detect_variants cnvkit_scatter_plot picard_metric_accumulation_level picard_metric_accumulation_level picard_metric_accumulation_level->alignment_and_qc picard_metric_accumulation_level merge_min_sv_size merge_min_sv_size merge_min_sv_size->sv_detect_variants merge_min_sv_size bcftools_merged_vcf bcftools_merged_vcf bcftools_merged_filtered_annotated_tsv bcftools_merged_filtered_annotated_tsv manta_all_candidates manta_all_candidates mark_duplicates_metrics mark_duplicates_metrics gc_bias_metrics_chart gc_bias_metrics_chart final_tsv final_tsv cnvkit_filtered_vcf cnvkit_filtered_vcf verify_bam_id_metrics verify_bam_id_metrics per_target_coverage_metrics per_target_coverage_metrics manta_somatic_variants manta_somatic_variants manta_small_candidates manta_small_candidates manta_diploid_variants manta_diploid_variants manta_filtered_vcf manta_filtered_vcf cnvnator_vcf cnvnator_vcf verify_bam_id_depth verify_bam_id_depth cn_diagram cn_diagram tumor_target_coverage tumor_target_coverage survivor_merged_vcf survivor_merged_vcf per_base_coverage_metrics per_base_coverage_metrics cnvkit_vcf cnvkit_vcf tumor_bin_level_ratios tumor_bin_level_ratios tumor_segmented_ratios tumor_segmented_ratios survivor_merged_annotated_tsv survivor_merged_annotated_tsv filtered_tsv filtered_tsv cnvnator_filtered_vcf cnvnator_filtered_vcf final_vcf final_vcf smoove_filtered_vcf smoove_filtered_vcf gc_bias_metrics gc_bias_metrics summary_hs_metrics summary_hs_metrics cnvnator_cn_file cnvnator_cn_file per_base_hs_metrics per_base_hs_metrics insert_size_histogram insert_size_histogram flagstats flagstats bcftools_merged_annotated_tsv bcftools_merged_annotated_tsv wgs_metrics wgs_metrics vep_summary vep_summary tumor_antitarget_coverage tumor_antitarget_coverage alignment_summary_metrics alignment_summary_metrics gc_bias_metrics_summary gc_bias_metrics_summary smoove_output_variants smoove_output_variants per_target_hs_metrics per_target_hs_metrics cnvnator_root cnvnator_root cram cram cn_scatter_plot cn_scatter_plot raw_vcf raw_vcf filtered_vcf filtered_vcf insert_size_metrics insert_size_metrics manta_tumor_only_variants manta_tumor_only_variants index_disclaimer_filtered_vcf vcf index index_disclaimer_filtered_vcf->filtered_vcf detect_variants->vep_summary detect_variants->raw_vcf detect_variants->add_disclaimer_filtered_tsv output_name detect_variants->add_disclaimer_filtered_tsv input_file detect_variants->add_disclaimer_final_vcf output_name detect_variants->add_disclaimer_final_vcf input_file detect_variants->add_disclaimer_filtered_vcf output_name detect_variants->add_disclaimer_filtered_vcf input_file detect_variants->add_disclaimer_final_tsv output_name detect_variants->add_disclaimer_final_tsv input_file detect_variants->sv_detect_variants snps_vcf add_disclaimer_filtered_tsv->filtered_tsv extract_freemix extract_freemix extract_freemix->detect_variants contamination_fraction index_cram samtools index cram index_cram->cram index_disclaimer_final_vcf vcf index add_disclaimer_final_vcf->index_disclaimer_final_vcf vcf add_disclaimer_survivor_sv_tsv->survivor_merged_annotated_tsv index_disclaimer_final_vcf->final_vcf add_disclaimer_bcftools_sv_tsv->bcftools_merged_annotated_tsv add_disclaimer_bcftools_filtered_sv_tsv->bcftools_merged_filtered_annotated_tsv add_disclaimer_filtered_vcf->index_disclaimer_filtered_vcf vcf alignment_and_qc->mark_duplicates_metrics alignment_and_qc->gc_bias_metrics_chart alignment_and_qc->verify_bam_id_metrics alignment_and_qc->per_target_coverage_metrics alignment_and_qc->verify_bam_id_depth alignment_and_qc->per_base_coverage_metrics alignment_and_qc->gc_bias_metrics alignment_and_qc->summary_hs_metrics alignment_and_qc->per_base_hs_metrics alignment_and_qc->insert_size_histogram alignment_and_qc->flagstats alignment_and_qc->wgs_metrics alignment_and_qc->alignment_summary_metrics alignment_and_qc->gc_bias_metrics_summary alignment_and_qc->per_target_hs_metrics alignment_and_qc->insert_size_metrics alignment_and_qc->detect_variants bam alignment_and_qc->extract_freemix verify_bam_id_metrics alignment_and_qc->bam_to_cram bam alignment_and_qc->sv_detect_variants bam add_disclaimer_survivor_sv_vcf->survivor_merged_vcf bam_to_cram->index_cram cram add_disclaimer_final_tsv->final_tsv add_disclaimer_bcftools_sv_vcf->bcftools_merged_vcf sv_detect_variants->manta_all_candidates sv_detect_variants->cnvkit_filtered_vcf sv_detect_variants->manta_somatic_variants sv_detect_variants->manta_small_candidates sv_detect_variants->manta_diploid_variants sv_detect_variants->manta_filtered_vcf sv_detect_variants->cnvnator_vcf sv_detect_variants->cn_diagram sv_detect_variants->tumor_target_coverage sv_detect_variants->cnvkit_vcf sv_detect_variants->tumor_bin_level_ratios sv_detect_variants->tumor_segmented_ratios sv_detect_variants->cnvnator_filtered_vcf sv_detect_variants->smoove_filtered_vcf sv_detect_variants->cnvnator_cn_file sv_detect_variants->tumor_antitarget_coverage sv_detect_variants->smoove_output_variants sv_detect_variants->cnvnator_root sv_detect_variants->cn_scatter_plot sv_detect_variants->manta_tumor_only_variants sv_detect_variants->add_disclaimer_survivor_sv_tsv output_name sv_detect_variants->add_disclaimer_survivor_sv_tsv input_file sv_detect_variants->add_disclaimer_bcftools_sv_tsv output_name sv_detect_variants->add_disclaimer_bcftools_sv_tsv input_file sv_detect_variants->add_disclaimer_bcftools_filtered_sv_tsv output_name sv_detect_variants->add_disclaimer_bcftools_filtered_sv_tsv input_file sv_detect_variants->add_disclaimer_survivor_sv_vcf output_name sv_detect_variants->add_disclaimer_survivor_sv_vcf input_file sv_detect_variants->add_disclaimer_bcftools_sv_vcf input_file sv_detect_variants->add_disclaimer_bcftools_sv_vcf output_name default1 1 default1->add_disclaimer_filtered_tsv line_number default2 2 default2->add_disclaimer_final_vcf line_number default3 1 default3->add_disclaimer_survivor_sv_tsv line_number default4 1 default4->add_disclaimer_bcftools_sv_tsv line_number default5 1 default5->add_disclaimer_bcftools_filtered_sv_tsv line_number default6 2 default6->add_disclaimer_filtered_vcf line_number default7 2 default7->add_disclaimer_survivor_sv_vcf line_number default8 1 default8->add_disclaimer_final_tsv line_number default9 2 default9->add_disclaimer_bcftools_sv_vcf line_number
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
ploidy Integer (Optional)
omni_vcf File
sequence https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/sequence_data.yml#sequence_data[] sequence: sequencing data and readgroup information

sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.

trimming https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/trimming_options.yml#trimming_options (Optional)
intervals 4a131458e43df0bbb3354b9afbfefde9[]
reference File
vep_plugins String[] (Optional)

array of plugins to use when running vep

qc_intervals File
cnvkit_method
gvcf_gq_bands String[]
manta_non_wgs Boolean (Optional)
merge_min_svs Integer
synonyms_file File (Optional)
vep_cache_dir Directory
bqsr_intervals String[] (Optional)
cnvkit_diagram Boolean (Optional)
blocklist_bedpe File (Optional)
cnvkit_vcf_name String (Optional)
disclaimer_text String (Optional)
merge_same_type Boolean
bqsr_known_sites File[]

One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.

merge_min_sv_size Integer
merge_same_strand Boolean
summary_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
manta_call_regions File (Optional)
merge_max_distance Integer
per_base_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
cnv_filter_min_size Integer (Optional)
cnvkit_scatter_plot Boolean (Optional)
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)
cnvkit_reference_cnn File (Optional)
manta_output_contigs Boolean (Optional)
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
vep_ensembl_assembly String

genome assembly to use in vep. Examples: GRCh38 or GRCm38

cnvkit_male_reference Boolean (Optional)
sv_filter_split_count Integer (Optional)
smoove_exclude_regions File (Optional)
sv_filter_paired_count Integer (Optional)
vep_custom_annotations https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[]

custom type, check types directory for input format

minimum_mapping_quality Integer (Optional)
cnvkit_drop_low_coverage Boolean (Optional)
variants_to_table_fields String[] (Optional)
cnv_filter_deletion_depth Double (Optional)
merge_estimate_sv_distance Boolean
variant_reporting_intervals File
cnv_filter_duplication_depth Double (Optional)
picard_metric_accumulation_level String
variants_to_table_genotype_fields String[] (Optional)
sv_filter_alt_abundance_percentage Double (Optional)

Steps

ID Runs Label Doc
index_cram
../tools/index_cram.cwl (CommandLineTool)
samtools index cram
bam_to_cram
../tools/bam_to_cram.cwl (CommandLineTool)
BAM to CRAM conversion
detect_variants exome alignment and germline variant detection
extract_freemix
germline_wgs.cwl#extract_freemix/6d4136a8-530f-443e-8ffd-0ef6911f37da (ExpressionTool)
alignment_and_qc
alignment_wgs.cwl (Workflow)
wgs alignment with qc
sv_detect_variants Subworkflow to allow calling different SV callers which require bam files as inputs
add_disclaimer_final_tsv
../tools/add_string_at_line.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a file
add_disclaimer_final_vcf
../tools/add_string_at_line_bgzipped.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a gzipped file
index_disclaimer_final_vcf
../tools/index_vcf.cwl (CommandLineTool)
vcf index
add_disclaimer_filtered_tsv
../tools/add_string_at_line.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a file
add_disclaimer_filtered_vcf
../tools/add_string_at_line_bgzipped.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a gzipped file
index_disclaimer_filtered_vcf
../tools/index_vcf.cwl (CommandLineTool)
vcf index
add_disclaimer_bcftools_sv_tsv
../tools/add_string_at_line.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a file
add_disclaimer_bcftools_sv_vcf
../tools/add_string_at_line_bgzipped.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a gzipped file
add_disclaimer_survivor_sv_tsv
../tools/add_string_at_line.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a file
add_disclaimer_survivor_sv_vcf
../tools/add_string_at_line_bgzipped.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a gzipped file
add_disclaimer_bcftools_filtered_sv_tsv
../tools/add_string_at_line.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a file

Outputs

ID Type Label Doc
cram File
raw_vcf File
final_tsv File
final_vcf File
flagstats File
cn_diagram File (Optional)
cnvkit_vcf File
vep_summary File
wgs_metrics File
cnvnator_vcf File
filtered_tsv File
filtered_vcf File
cnvnator_root File
cn_scatter_plot File (Optional)
gc_bias_metrics File
cnvnator_cn_file File
manta_filtered_vcf File
summary_hs_metrics File[]
bcftools_merged_vcf File
cnvkit_filtered_vcf File
insert_size_metrics File
per_base_hs_metrics File[]
smoove_filtered_vcf File
survivor_merged_vcf File
verify_bam_id_depth File
manta_all_candidates File
cnvnator_filtered_vcf File
gc_bias_metrics_chart File
insert_size_histogram File
per_target_hs_metrics File[]
tumor_target_coverage File
verify_bam_id_metrics File
manta_diploid_variants File (Optional)
manta_small_candidates File
manta_somatic_variants File (Optional)
smoove_output_variants File
tumor_bin_level_ratios File
tumor_segmented_ratios File
gc_bias_metrics_summary File
mark_duplicates_metrics File
alignment_summary_metrics File
manta_tumor_only_variants File (Optional)
per_base_coverage_metrics File[]
tumor_antitarget_coverage File
per_target_coverage_metrics File[]
bcftools_merged_annotated_tsv File
survivor_merged_annotated_tsv File
bcftools_merged_filtered_annotated_tsv File
Permalink: https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/pipelines/germline_wgs.cwl