Workflow: exome alignment and somatic variant detection

Fetched 2023-01-12 04:22:50 GMT
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workflow cluster_outputs Workflow Outputs cluster_inputs Workflow Inputs picard_metric_accumulation_level picard_metric_accumulation_level tumor_alignment_and_qc exome alignment with qc picard_metric_accumulation_level->tumor_alignment_and_qc picard_metric_accumulation_level normal_alignment_and_qc exome alignment with qc picard_metric_accumulation_level->normal_alignment_and_qc picard_metric_accumulation_level per_target_intervals per_target_intervals per_target_intervals->tumor_alignment_and_qc per_target_intervals per_target_intervals->normal_alignment_and_qc per_target_intervals custom_gnomad_vcf custom_gnomad_vcf detect_variants Detect Variants workflow custom_gnomad_vcf->detect_variants custom_gnomad_vcf tumor_readgroups tumor_readgroups tumor_readgroups->tumor_alignment_and_qc readgroups variants_to_table_genotype_fields variants_to_table_genotype_fields variants_to_table_genotype_fields->detect_variants variants_to_table_genotype_fields vep_cache_dir vep_cache_dir vep_cache_dir->detect_variants vep_cache_dir varscan_strand_filter varscan_strand_filter varscan_strand_filter->detect_variants varscan_strand_filter normal_bams normal_bams normal_bams->normal_alignment_and_qc bams mutect_max_alt_allele_in_normal_fraction mutect_max_alt_allele_in_normal_fraction mutect_max_alt_allele_in_normal_fraction->detect_variants mutect_max_alt_allele_in_normal_fraction interval_list interval_list interval_list->detect_variants interval_list reference reference reference->detect_variants reference reference->tumor_alignment_and_qc reference reference->normal_alignment_and_qc reference normal_readgroups normal_readgroups normal_readgroups->normal_alignment_and_qc readgroups coding_only coding_only coding_only->detect_variants coding_only mutect_artifact_detection_mode mutect_artifact_detection_mode mutect_artifact_detection_mode->detect_variants mutect_artifact_detection_mode variants_to_table_fields variants_to_table_fields variants_to_table_fields->detect_variants variants_to_table_fields minimum_base_quality minimum_base_quality minimum_base_quality->tumor_alignment_and_qc minimum_base_quality minimum_base_quality->normal_alignment_and_qc minimum_base_quality per_target_bait_intervals per_target_bait_intervals per_target_bait_intervals->tumor_alignment_and_qc per_target_bait_intervals per_target_bait_intervals->normal_alignment_and_qc per_target_bait_intervals bait_intervals bait_intervals bait_intervals->tumor_alignment_and_qc bait_intervals bait_intervals->normal_alignment_and_qc bait_intervals varscan_min_var_freq varscan_min_var_freq varscan_min_var_freq->detect_variants varscan_min_var_freq vep_to_table_fields vep_to_table_fields vep_to_table_fields->detect_variants vep_to_table_fields omni_vcf omni_vcf omni_vcf->tumor_alignment_and_qc omni_vcf omni_vcf->normal_alignment_and_qc omni_vcf synonyms_file synonyms_file synonyms_file->detect_variants synonyms_file varscan_p_value varscan_p_value varscan_p_value->detect_variants varscan_p_value cle_vcf_filter cle_vcf_filter cle_vcf_filter->detect_variants cle_vcf_filter mills mills mills->tumor_alignment_and_qc mills mills->normal_alignment_and_qc mills per_base_bait_intervals per_base_bait_intervals per_base_bait_intervals->tumor_alignment_and_qc per_base_bait_intervals per_base_bait_intervals->normal_alignment_and_qc per_base_bait_intervals mutect_scatter_count mutect_scatter_count mutect_scatter_count->detect_variants mutect_scatter_count pindel_insert_size pindel_insert_size pindel_insert_size->detect_variants pindel_insert_size per_base_intervals per_base_intervals per_base_intervals->tumor_alignment_and_qc per_base_intervals per_base_intervals->normal_alignment_and_qc per_base_intervals strelka_cpu_reserved strelka_cpu_reserved strelka_cpu_reserved->detect_variants strelka_cpu_reserved varscan_min_coverage varscan_min_coverage varscan_min_coverage->detect_variants varscan_min_coverage panel_of_normals_vcf panel_of_normals_vcf panel_of_normals_vcf->detect_variants panel_of_normals_vcf known_indels known_indels known_indels->tumor_alignment_and_qc known_indels known_indels->normal_alignment_and_qc known_indels dbsnp dbsnp dbsnp->tumor_alignment_and_qc dbsnp dbsnp->normal_alignment_and_qc dbsnp varscan_max_normal_freq varscan_max_normal_freq varscan_max_normal_freq->detect_variants varscan_max_normal_freq dbsnp_vcf dbsnp_vcf dbsnp_vcf->detect_variants dbsnp_vcf cosmic_vcf cosmic_vcf cosmic_vcf->detect_variants cosmic_vcf mutect_max_alt_alleles_in_normal_count mutect_max_alt_alleles_in_normal_count mutect_max_alt_alleles_in_normal_count->detect_variants mutect_max_alt_alleles_in_normal_count minimum_mapping_quality minimum_mapping_quality minimum_mapping_quality->tumor_alignment_and_qc minimum_mapping_quality minimum_mapping_quality->normal_alignment_and_qc minimum_mapping_quality hgvs_annotation hgvs_annotation hgvs_annotation->detect_variants hgvs_annotation target_intervals target_intervals target_intervals->tumor_alignment_and_qc target_intervals target_intervals->normal_alignment_and_qc target_intervals bqsr_intervals bqsr_intervals bqsr_intervals->tumor_alignment_and_qc bqsr_intervals bqsr_intervals->normal_alignment_and_qc bqsr_intervals docm_vcf docm_vcf docm_vcf->detect_variants docm_vcf tumor_bams tumor_bams tumor_bams->tumor_alignment_and_qc bams normal_verify_bam_id_metrics normal_verify_bam_id_metrics tumor_per_target_hs_metrics tumor_per_target_hs_metrics final_vcf final_vcf tumor_bam_readcount_tsv tumor_bam_readcount_tsv strelka_filtered_vcf strelka_filtered_vcf normal_per_target_coverage_metrics normal_per_target_coverage_metrics mutect_unfiltered_vcf mutect_unfiltered_vcf strelka_unfiltered_vcf strelka_unfiltered_vcf tumor_verify_bam_id_depth tumor_verify_bam_id_depth tumor_verify_bam_id_metrics tumor_verify_bam_id_metrics docm_unfiltered_vcf docm_unfiltered_vcf pindel_unfiltered_vcf pindel_unfiltered_vcf normal_verify_bam_id_depth normal_verify_bam_id_depth tumor_hs_metrics tumor_hs_metrics tumor_alignment_summary_metrics tumor_alignment_summary_metrics tumor_per_base_coverage_metrics tumor_per_base_coverage_metrics normal_mark_duplicates_metrics normal_mark_duplicates_metrics tumor_flagstats tumor_flagstats docm_filtered_vcf docm_filtered_vcf tumor_insert_size_metrics tumor_insert_size_metrics normal_insert_size_metrics normal_insert_size_metrics normal_hs_metrics normal_hs_metrics varscan_filtered_vcf varscan_filtered_vcf final_filtered_vcf final_filtered_vcf tumor_cram tumor_cram tumor_mark_duplicates_metrics tumor_mark_duplicates_metrics normal_flagstats normal_flagstats mutect_filtered_vcf mutect_filtered_vcf normal_per_base_coverage_metrics normal_per_base_coverage_metrics normal_per_target_hs_metrics normal_per_target_hs_metrics normal_cram normal_cram tumor_per_target_coverage_metrics tumor_per_target_coverage_metrics normal_per_base_hs_metrics normal_per_base_hs_metrics normal_alignment_summary_metrics normal_alignment_summary_metrics varscan_unfiltered_vcf varscan_unfiltered_vcf pindel_filtered_vcf pindel_filtered_vcf normal_bam_readcount_tsv normal_bam_readcount_tsv vep_summary vep_summary final_tsv final_tsv tumor_per_base_hs_metrics tumor_per_base_hs_metrics detect_variants->final_vcf detect_variants->tumor_bam_readcount_tsv detect_variants->strelka_filtered_vcf detect_variants->mutect_unfiltered_vcf detect_variants->strelka_unfiltered_vcf detect_variants->docm_unfiltered_vcf detect_variants->pindel_unfiltered_vcf detect_variants->docm_filtered_vcf detect_variants->varscan_filtered_vcf detect_variants->final_filtered_vcf detect_variants->mutect_filtered_vcf detect_variants->varscan_unfiltered_vcf detect_variants->pindel_filtered_vcf detect_variants->normal_bam_readcount_tsv detect_variants->vep_summary detect_variants->final_tsv tumor_alignment_and_qc->tumor_per_target_hs_metrics tumor_alignment_and_qc->tumor_verify_bam_id_depth tumor_alignment_and_qc->tumor_verify_bam_id_metrics tumor_alignment_and_qc->tumor_hs_metrics tumor_alignment_and_qc->tumor_alignment_summary_metrics tumor_alignment_and_qc->tumor_per_base_coverage_metrics tumor_alignment_and_qc->tumor_flagstats tumor_alignment_and_qc->tumor_insert_size_metrics tumor_alignment_and_qc->tumor_cram tumor_alignment_and_qc->tumor_mark_duplicates_metrics tumor_alignment_and_qc->tumor_per_target_coverage_metrics tumor_alignment_and_qc->tumor_per_base_hs_metrics tumor_alignment_and_qc->detect_variants tumor_cram normal_alignment_and_qc->normal_verify_bam_id_metrics normal_alignment_and_qc->normal_per_target_coverage_metrics normal_alignment_and_qc->normal_verify_bam_id_depth normal_alignment_and_qc->normal_mark_duplicates_metrics normal_alignment_and_qc->normal_insert_size_metrics normal_alignment_and_qc->normal_hs_metrics normal_alignment_and_qc->normal_flagstats normal_alignment_and_qc->normal_per_base_coverage_metrics normal_alignment_and_qc->normal_per_target_hs_metrics normal_alignment_and_qc->normal_cram normal_alignment_and_qc->normal_per_base_hs_metrics normal_alignment_and_qc->normal_alignment_summary_metrics normal_alignment_and_qc->detect_variants normal_cram default1 true default1->detect_variants strelka_exome_mode
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Inputs

ID Type Title Doc
dbsnp File
mills File
docm_vcf File
omni_vcf File
dbsnp_vcf File (Optional)
reference String
cosmic_vcf File (Optional)
tumor_bams File[]
coding_only Boolean (Optional)
normal_bams File[]
known_indels File
interval_list File
synonyms_file File (Optional)
vep_cache_dir String (Optional)
bait_intervals File
bqsr_intervals String[]
cle_vcf_filter Boolean
hgvs_annotation Boolean (Optional)
varscan_p_value Float (Optional)
target_intervals File
tumor_readgroups String[]
custom_gnomad_vcf File (Optional)
normal_readgroups String[]
per_base_intervals File
pindel_insert_size Integer
vep_to_table_fields String[]
minimum_base_quality Integer (Optional)
mutect_scatter_count Integer
panel_of_normals_vcf File (Optional)
per_target_intervals File
strelka_cpu_reserved Integer (Optional)
varscan_min_coverage Integer (Optional)
varscan_min_var_freq Float (Optional)
varscan_strand_filter Integer (Optional)
minimum_mapping_quality Integer (Optional)
per_base_bait_intervals File
varscan_max_normal_freq Float (Optional)
variants_to_table_fields String[]
per_target_bait_intervals File
mutect_artifact_detection_mode Boolean
picard_metric_accumulation_level String
variants_to_table_genotype_fields String[]
mutect_max_alt_alleles_in_normal_count Integer (Optional)
mutect_max_alt_allele_in_normal_fraction Float (Optional)

Steps

ID Runs Label Doc
detect_variants Detect Variants workflow
tumor_alignment_and_qc
exome_alignment.cwl (Workflow)
exome alignment with qc
normal_alignment_and_qc
exome_alignment.cwl (Workflow)
exome alignment with qc

Outputs

ID Type Label Doc
final_tsv File
final_vcf File
tumor_cram File
normal_cram File
vep_summary File
tumor_flagstats File
normal_flagstats File
tumor_hs_metrics File
docm_filtered_vcf File
normal_hs_metrics 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
tumor_insert_size_metrics File
tumor_per_base_hs_metrics File (Optional)
tumor_verify_bam_id_depth File
normal_insert_size_metrics File
normal_per_base_hs_metrics File (Optional)
normal_verify_bam_id_depth File
tumor_per_target_hs_metrics File (Optional)
tumor_verify_bam_id_metrics File
normal_per_target_hs_metrics File (Optional)
normal_verify_bam_id_metrics File
tumor_mark_duplicates_metrics File
normal_mark_duplicates_metrics File
tumor_alignment_summary_metrics File
tumor_per_base_coverage_metrics File (Optional)
normal_alignment_summary_metrics File
normal_per_base_coverage_metrics File (Optional)
tumor_per_target_coverage_metrics File (Optional)
normal_per_target_coverage_metrics File (Optional)
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Permalink: https://w3id.org/cwl/view/git/bc4a0f74082ffcf099977a1efac830d7e100bd66/somatic_exome_workflow.cwl