Workflow: exome alignment and somatic variant detection for cle purpose

Fetched 2023-01-09 23:10:04 GMT
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workflow cluster_outputs Workflow Outputs cluster_inputs Workflow Inputs filter_somatic_llr_tumor_purity filter_somatic_llr_tumor_purity detect_variants Detect Variants workflow filter_somatic_llr_tumor_purity->detect_variants filter_somatic_llr_tumor_purity disclaimer_version disclaimer_version add_disclaimer_version_to_final_tsv Insert an arbitrary string at a specific line of a file disclaimer_version->add_disclaimer_version_to_final_tsv some_text add_disclaimer_version_to_final_filtered_vcf Insert an arbitrary string at a specific line of a gzipped file disclaimer_version->add_disclaimer_version_to_final_filtered_vcf some_text tumor_name tumor_name tumor_alignment_and_qc exome alignment with qc tumor_name->tumor_alignment_and_qc final_name per_target_intervals per_target_intervals normal_alignment_and_qc exome alignment with qc per_target_intervals->normal_alignment_and_qc per_target_intervals per_target_intervals->tumor_alignment_and_qc per_target_intervals summary_intervals summary_intervals summary_intervals->normal_alignment_and_qc summary_intervals summary_intervals->tumor_alignment_and_qc summary_intervals reference reference reference->normal_alignment_and_qc reference tumor_bam_to_cram BAM to CRAM conversion reference->tumor_bam_to_cram reference concordance Concordance checking between Tumor and Normal BAM reference->concordance reference reference->detect_variants reference normal_bam_to_cram BAM to CRAM conversion reference->normal_bam_to_cram reference reference->tumor_alignment_and_qc reference cle_vcf_filter cle_vcf_filter cle_vcf_filter->detect_variants cle_vcf_filter vep_to_table_fields vep_to_table_fields vep_to_table_fields->detect_variants vep_to_table_fields synonyms_file synonyms_file synonyms_file->detect_variants synonyms_file disclaimer_text disclaimer_text add_disclaimer_to_final_tsv Insert an arbitrary string at a specific line of a file disclaimer_text->add_disclaimer_to_final_tsv some_text add_disclaimer_to_final_filtered_vcf Insert an arbitrary string at a specific line of a gzipped file disclaimer_text->add_disclaimer_to_final_filtered_vcf some_text strelka_cpu_reserved strelka_cpu_reserved strelka_cpu_reserved->detect_variants strelka_cpu_reserved varscan_p_value varscan_p_value varscan_p_value->detect_variants varscan_p_value bait_intervals bait_intervals bait_intervals->normal_alignment_and_qc bait_intervals bait_intervals->tumor_alignment_and_qc bait_intervals annotate_coding_only annotate_coding_only annotate_coding_only->detect_variants annotate_coding_only vep_ensembl_species vep_ensembl_species vep_ensembl_species->detect_variants vep_ensembl_species vep_cache_dir vep_cache_dir vep_cache_dir->detect_variants vep_cache_dir omni_vcf omni_vcf omni_vcf->normal_alignment_and_qc omni_vcf omni_vcf->tumor_alignment_and_qc omni_vcf picard_metric_accumulation_level picard_metric_accumulation_level picard_metric_accumulation_level->normal_alignment_and_qc picard_metric_accumulation_level picard_metric_accumulation_level->tumor_alignment_and_qc picard_metric_accumulation_level normal_sample_name normal_sample_name normal_sample_name->detect_variants normal_sample_name target_interval_padding target_interval_padding pad_target_intervals expand interval list regions by a given number of basepairs target_interval_padding->pad_target_intervals roi_padding varscan_min_coverage varscan_min_coverage varscan_min_coverage->detect_variants varscan_min_coverage target_intervals target_intervals: interval_list file of targets used in the sequencing experiment target_intervals->normal_alignment_and_qc target_intervals target_intervals->tumor_alignment_and_qc target_intervals target_intervals->pad_target_intervals interval_list normal_sequence normal_sequence: WT sequencing data and readgroup information normal_sequence->normal_alignment_and_qc sequence vep_custom_annotations vep_custom_annotations vep_custom_annotations->detect_variants vep_custom_annotations somalier_vcf somalier_vcf somalier_vcf->concordance vcf variants_to_table_fields variants_to_table_fields variants_to_table_fields->detect_variants variants_to_table_fields vep_ensembl_assembly vep_ensembl_assembly vep_ensembl_assembly->detect_variants vep_ensembl_assembly variants_to_table_genotype_fields variants_to_table_genotype_fields variants_to_table_genotype_fields->detect_variants variants_to_table_genotype_fields docm_vcf docm_vcf docm_vcf->detect_variants docm_vcf normal_name normal_name normal_name->normal_alignment_and_qc final_name per_base_intervals per_base_intervals per_base_intervals->normal_alignment_and_qc per_base_intervals per_base_intervals->tumor_alignment_and_qc per_base_intervals bqsr_known_sites bqsr_known_sites bqsr_known_sites->normal_alignment_and_qc bqsr_known_sites bqsr_known_sites->tumor_alignment_and_qc bqsr_known_sites filter_docm_variants filter_docm_variants filter_docm_variants->detect_variants filter_docm_variants tumor_sequence tumor_sequence: MT sequencing data and readgroup information tumor_sequence->tumor_alignment_and_qc sequence pindel_insert_size pindel_insert_size pindel_insert_size->detect_variants pindel_insert_size varscan_strand_filter varscan_strand_filter varscan_strand_filter->detect_variants varscan_strand_filter filter_somatic_llr_threshold filter_somatic_llr_threshold filter_somatic_llr_threshold->detect_variants filter_somatic_llr_threshold vep_pick vep_pick vep_pick->detect_variants vep_pick tumor_sample_name tumor_sample_name tumor_sample_name->detect_variants tumor_sample_name filter_minimum_depth filter_minimum_depth filter_minimum_depth->detect_variants filter_minimum_depth qc_minimum_mapping_quality qc_minimum_mapping_quality qc_minimum_mapping_quality->normal_alignment_and_qc qc_minimum_mapping_quality qc_minimum_mapping_quality->tumor_alignment_and_qc qc_minimum_mapping_quality filter_somatic_llr_normal_contamination_rate filter_somatic_llr_normal_contamination_rate filter_somatic_llr_normal_contamination_rate->detect_variants filter_somatic_llr_normal_contamination_rate varscan_max_normal_freq varscan_max_normal_freq varscan_max_normal_freq->detect_variants varscan_max_normal_freq bqsr_intervals bqsr_intervals bqsr_intervals->normal_alignment_and_qc bqsr_intervals bqsr_intervals->tumor_alignment_and_qc bqsr_intervals vep_ensembl_version vep_ensembl_version vep_ensembl_version->detect_variants vep_ensembl_version scatter_count scatter_count scatter_count->detect_variants scatter_count varscan_min_var_freq varscan_min_var_freq varscan_min_var_freq->detect_variants varscan_min_var_freq qc_minimum_base_quality qc_minimum_base_quality qc_minimum_base_quality->normal_alignment_and_qc qc_minimum_base_quality qc_minimum_base_quality->tumor_alignment_and_qc qc_minimum_base_quality tumor_per_target_coverage_metrics tumor_per_target_coverage_metrics tumor_hs_metrics tumor_hs_metrics tumor_summary_hs_metrics tumor_summary_hs_metrics tumor_insert_size_metrics tumor_insert_size_metrics somalier_concordance_metrics somalier_concordance_metrics tumor_alignment_summary_metrics tumor_alignment_summary_metrics varscan_filtered_vcf varscan_filtered_vcf normal_mark_duplicates_metrics normal_mark_duplicates_metrics normal_flagstats normal_flagstats final_vcf final_vcf mutect_filtered_vcf mutect_filtered_vcf tumor_mark_duplicates_metrics tumor_mark_duplicates_metrics docm_filtered_vcf docm_filtered_vcf pindel_filtered_vcf pindel_filtered_vcf normal_alignment_summary_metrics normal_alignment_summary_metrics normal_hs_metrics normal_hs_metrics tumor_snv_bam_readcount_tsv tumor_snv_bam_readcount_tsv final_filtered_vcf final_filtered_vcf tumor_per_target_hs_metrics tumor_per_target_hs_metrics tumor_verify_bam_id_depth tumor_verify_bam_id_depth normal_snv_bam_readcount_tsv normal_snv_bam_readcount_tsv tumor_per_base_hs_metrics tumor_per_base_hs_metrics tumor_per_base_coverage_metrics tumor_per_base_coverage_metrics normal_per_target_hs_metrics normal_per_target_hs_metrics normal_insert_size_metrics normal_insert_size_metrics normal_summary_hs_metrics normal_summary_hs_metrics normal_verify_bam_id_metrics normal_verify_bam_id_metrics normal_verify_bam_id_depth normal_verify_bam_id_depth normal_cram normal_cram tumor_cram tumor_cram pindel_unfiltered_vcf pindel_unfiltered_vcf normal_per_base_hs_metrics normal_per_base_hs_metrics strelka_unfiltered_vcf strelka_unfiltered_vcf tumor_indel_bam_readcount_tsv tumor_indel_bam_readcount_tsv normal_indel_bam_readcount_tsv normal_indel_bam_readcount_tsv vep_summary vep_summary somalier_concordance_statistics somalier_concordance_statistics varscan_unfiltered_vcf varscan_unfiltered_vcf mutect_unfiltered_vcf mutect_unfiltered_vcf strelka_filtered_vcf strelka_filtered_vcf normal_per_base_coverage_metrics normal_per_base_coverage_metrics normal_per_target_coverage_metrics normal_per_target_coverage_metrics final_tsv final_tsv tumor_flagstats tumor_flagstats tumor_verify_bam_id_metrics tumor_verify_bam_id_metrics normal_index_cram samtools index cram normal_index_cram->normal_cram normal_alignment_and_qc->normal_mark_duplicates_metrics normal_alignment_and_qc->normal_flagstats normal_alignment_and_qc->normal_alignment_summary_metrics normal_alignment_and_qc->normal_hs_metrics normal_alignment_and_qc->normal_per_target_hs_metrics normal_alignment_and_qc->normal_insert_size_metrics normal_alignment_and_qc->normal_summary_hs_metrics normal_alignment_and_qc->normal_verify_bam_id_metrics normal_alignment_and_qc->normal_verify_bam_id_depth normal_alignment_and_qc->normal_per_base_hs_metrics normal_alignment_and_qc->normal_per_base_coverage_metrics normal_alignment_and_qc->normal_per_target_coverage_metrics normal_alignment_and_qc->concordance bam_2 normal_alignment_and_qc->detect_variants normal_bam normal_alignment_and_qc->normal_bam_to_cram bam add_disclaimer_to_final_tsv->add_disclaimer_version_to_final_tsv input_file add_disclaimer_to_final_tsv->add_disclaimer_version_to_final_tsv output_name tumor_index_cram samtools index cram tumor_bam_to_cram->tumor_index_cram cram add_disclaimer_version_to_final_tsv->final_tsv concordance->somalier_concordance_metrics concordance->somalier_concordance_statistics detect_variants->varscan_filtered_vcf detect_variants->final_vcf detect_variants->mutect_filtered_vcf detect_variants->docm_filtered_vcf detect_variants->pindel_filtered_vcf detect_variants->tumor_snv_bam_readcount_tsv detect_variants->normal_snv_bam_readcount_tsv detect_variants->pindel_unfiltered_vcf detect_variants->strelka_unfiltered_vcf detect_variants->tumor_indel_bam_readcount_tsv detect_variants->normal_indel_bam_readcount_tsv detect_variants->vep_summary detect_variants->varscan_unfiltered_vcf detect_variants->mutect_unfiltered_vcf detect_variants->strelka_filtered_vcf detect_variants->add_disclaimer_to_final_tsv output_name detect_variants->add_disclaimer_to_final_tsv input_file detect_variants->add_disclaimer_to_final_filtered_vcf input_file detect_variants->add_disclaimer_to_final_filtered_vcf output_name normal_bam_to_cram->normal_index_cram cram tumor_alignment_and_qc->tumor_per_target_coverage_metrics tumor_alignment_and_qc->tumor_hs_metrics tumor_alignment_and_qc->tumor_summary_hs_metrics tumor_alignment_and_qc->tumor_insert_size_metrics tumor_alignment_and_qc->tumor_alignment_summary_metrics tumor_alignment_and_qc->tumor_mark_duplicates_metrics tumor_alignment_and_qc->tumor_per_target_hs_metrics tumor_alignment_and_qc->tumor_verify_bam_id_depth tumor_alignment_and_qc->tumor_per_base_hs_metrics tumor_alignment_and_qc->tumor_per_base_coverage_metrics tumor_alignment_and_qc->tumor_flagstats tumor_alignment_and_qc->tumor_verify_bam_id_metrics tumor_alignment_and_qc->tumor_bam_to_cram bam tumor_alignment_and_qc->concordance bam_1 tumor_alignment_and_qc->detect_variants tumor_bam add_disclaimer_to_final_filtered_vcf->add_disclaimer_version_to_final_filtered_vcf output_name add_disclaimer_to_final_filtered_vcf->add_disclaimer_version_to_final_filtered_vcf input_file annotated_filter_vcf_index vcf index add_disclaimer_version_to_final_filtered_vcf->annotated_filter_vcf_index vcf annotated_filter_vcf_index->final_filtered_vcf tumor_index_cram->tumor_cram pad_target_intervals->detect_variants roi_intervals default1 1 default1->add_disclaimer_to_final_tsv line_number default2 2 default2->add_disclaimer_version_to_final_tsv line_number default3 true default3->detect_variants strelka_exome_mode default4 2 default4->add_disclaimer_to_final_filtered_vcf line_number default5 3 default5->add_disclaimer_version_to_final_filtered_vcf line_number
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Inputs

ID Type Title Doc
docm_vcf File
omni_vcf File
vep_pick
reference String
tumor_name String (Optional)
normal_name String (Optional)
somalier_vcf File
scatter_count Integer

scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs

synonyms_file File (Optional)
vep_cache_dir Directory
bait_intervals File
bqsr_intervals String[]
cle_vcf_filter Boolean
tumor_sequence https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/sequence_data.yml#sequence_data[] tumor_sequence: MT sequencing data and readgroup information

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

disclaimer_text String (Optional)
normal_sequence https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/sequence_data.yml#sequence_data[] normal_sequence: WT sequencing data and readgroup information

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

varscan_p_value Float (Optional)
bqsr_known_sites File[]

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

target_intervals File target_intervals: interval_list file of targets used in the sequencing experiment

target_intervals is an interval_list corresponding to the targets for the capture reagent. BED files with this information can be converted to interval_lists with Picard BedToIntervalList. In general for a WES exome reagent bait_intervals and target_intervals are the same.

summary_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
tumor_sample_name String
disclaimer_version String
normal_sample_name String
per_base_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
pindel_insert_size Integer
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_docm_variants Boolean (Optional)
filter_minimum_depth Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[]
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)
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

qc_minimum_base_quality Integer (Optional)
target_interval_padding Integer target_interval_padding

The effective coverage of capture products generally extends out beyond the actual regions targeted. This parameter allows variants to be called in these wingspan regions, extending this many base pairs from each side of the target regions.

varscan_max_normal_freq Float (Optional)
variants_to_table_fields String[]
qc_minimum_mapping_quality Integer (Optional)
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.

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

picard_metric_accumulation_level String
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
concordance
../tools/concordance.cwl (CommandLineTool)
Concordance checking between Tumor and Normal BAM
detect_variants
detect_variants.cwl (Workflow)
Detect Variants workflow
tumor_index_cram
../tools/index_cram.cwl (CommandLineTool)
samtools index cram
normal_index_cram
../tools/index_cram.cwl (CommandLineTool)
samtools index cram
tumor_bam_to_cram
../tools/bam_to_cram.cwl (CommandLineTool)
BAM to CRAM conversion
normal_bam_to_cram
../tools/bam_to_cram.cwl (CommandLineTool)
BAM to CRAM conversion
pad_target_intervals
../tools/interval_list_expand.cwl (CommandLineTool)
expand interval list regions by a given number of basepairs
tumor_alignment_and_qc
alignment_exome.cwl (Workflow)
exome alignment with qc
normal_alignment_and_qc
alignment_exome.cwl (Workflow)
exome alignment with qc
annotated_filter_vcf_index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
add_disclaimer_to_final_tsv
../tools/add_string_at_line.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a file
add_disclaimer_version_to_final_tsv
../tools/add_string_at_line.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a file
add_disclaimer_to_final_filtered_vcf
../tools/add_string_at_line_bgzipped.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a gzipped file
add_disclaimer_version_to_final_filtered_vcf
../tools/add_string_at_line_bgzipped.cwl (CommandLineTool)
Insert an arbitrary string at a specific line of a gzipped file

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
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_summary_hs_metrics File[]
normal_summary_hs_metrics File[]
tumor_insert_size_metrics File
tumor_per_base_hs_metrics File[]
tumor_verify_bam_id_depth File
normal_insert_size_metrics File
normal_per_base_hs_metrics File[]
normal_verify_bam_id_depth File
tumor_per_target_hs_metrics File[]
tumor_snv_bam_readcount_tsv File
tumor_verify_bam_id_metrics File
normal_per_target_hs_metrics File[]
normal_snv_bam_readcount_tsv File
normal_verify_bam_id_metrics File
somalier_concordance_metrics File
tumor_indel_bam_readcount_tsv File
tumor_mark_duplicates_metrics File
normal_indel_bam_readcount_tsv File
normal_mark_duplicates_metrics File
somalier_concordance_statistics File
tumor_alignment_summary_metrics File
tumor_per_base_coverage_metrics File[]
normal_alignment_summary_metrics File
normal_per_base_coverage_metrics File[]
tumor_per_target_coverage_metrics File[]
normal_per_target_coverage_metrics File[]
Permalink: https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/pipelines/somatic_exome_cle.cwl