Workflow: somatic_exome: exome alignment and somatic variant detection

Fetched 2023-01-09 23:29:06 GMT

somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml

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workflow cluster_outputs Workflow Outputs cluster_inputs Workflow Inputs reference reference: Reference fasta file for a desired assembly tumor_alignment_and_qc exome alignment with qc reference->tumor_alignment_and_qc reference normal_alignment_and_qc exome alignment with qc reference->normal_alignment_and_qc reference cnvkit cnvkit reference->cnvkit reference manta Set up and execute manta reference->manta reference concordance Concordance checking between Tumor and Normal BAM reference->concordance reference detect_variants Detect Variants workflow reference->detect_variants reference normal_bam_to_cram BAM to CRAM conversion reference->normal_bam_to_cram reference tumor_bam_to_cram BAM to CRAM conversion reference->tumor_bam_to_cram reference target_intervals target_intervals: interval_list file of targets used in the sequencing experiment target_intervals->tumor_alignment_and_qc target_intervals target_intervals->normal_alignment_and_qc target_intervals pad_target_intervals expand interval list regions by a given number of basepairs target_intervals->pad_target_intervals interval_list tumor_sequence tumor_sequence: MT sequencing data and readgroup information tumor_sequence->tumor_alignment_and_qc sequence strelka_cpu_reserved strelka_cpu_reserved strelka_cpu_reserved->detect_variants strelka_cpu_reserved vep_pick vep_pick vep_pick->detect_variants vep_pick summary_intervals summary_intervals summary_intervals->tumor_alignment_and_qc summary_intervals summary_intervals->normal_alignment_and_qc summary_intervals vep_ensembl_assembly vep_ensembl_assembly vep_ensembl_assembly->detect_variants vep_ensembl_assembly bqsr_intervals bqsr_intervals: Array of strings specifying regions for base quality score recalibration bqsr_intervals->tumor_alignment_and_qc bqsr_intervals bqsr_intervals->normal_alignment_and_qc bqsr_intervals filter_docm_variants filter_docm_variants filter_docm_variants->detect_variants filter_docm_variants variants_to_table_fields variants_to_table_fields variants_to_table_fields->detect_variants variants_to_table_fields vep_cache_dir vep_cache_dir vep_cache_dir->detect_variants vep_cache_dir tumor_sample_name tumor_sample_name tumor_sample_name->detect_variants tumor_sample_name picard_metric_accumulation_level picard_metric_accumulation_level picard_metric_accumulation_level->tumor_alignment_and_qc picard_metric_accumulation_level picard_metric_accumulation_level->normal_alignment_and_qc picard_metric_accumulation_level bait_intervals bait_intervals: interval_list file of baits used in the sequencing experiment bait_intervals->tumor_alignment_and_qc bait_intervals bait_intervals->normal_alignment_and_qc bait_intervals bait_intervals->cnvkit bait_intervals trimming trimming trimming->tumor_alignment_and_qc trimming trimming->normal_alignment_and_qc trimming per_base_intervals per_base_intervals: additional intervals over which to summarize coverage/QC at a per-base resolution per_base_intervals->tumor_alignment_and_qc per_base_intervals per_base_intervals->normal_alignment_and_qc per_base_intervals pindel_insert_size pindel_insert_size pindel_insert_size->detect_variants pindel_insert_size manta_call_regions manta_call_regions manta_call_regions->manta call_regions somalier_vcf somalier_vcf somalier_vcf->concordance vcf qc_minimum_base_quality qc_minimum_base_quality qc_minimum_base_quality->tumor_alignment_and_qc qc_minimum_base_quality qc_minimum_base_quality->normal_alignment_and_qc qc_minimum_base_quality per_target_intervals per_target_intervals: additional intervals over which to summarize coverage/QC at a per-target resolution per_target_intervals->tumor_alignment_and_qc per_target_intervals per_target_intervals->normal_alignment_and_qc per_target_intervals vep_ensembl_species vep_ensembl_species vep_ensembl_species->detect_variants vep_ensembl_species variants_to_table_genotype_fields variants_to_table_genotype_fields variants_to_table_genotype_fields->detect_variants variants_to_table_genotype_fields varscan_strand_filter varscan_strand_filter varscan_strand_filter->detect_variants varscan_strand_filter vep_ensembl_version vep_ensembl_version vep_ensembl_version->detect_variants vep_ensembl_version omni_vcf omni_vcf omni_vcf->tumor_alignment_and_qc omni_vcf omni_vcf->normal_alignment_and_qc omni_vcf varscan_min_var_freq varscan_min_var_freq varscan_min_var_freq->detect_variants varscan_min_var_freq filter_somatic_llr_threshold filter_somatic_llr_threshold filter_somatic_llr_threshold->detect_variants filter_somatic_llr_threshold validated_variants validated_variants validated_variants->detect_variants validated_variants scatter_count scatter_count scatter_count->detect_variants scatter_count vep_custom_annotations vep_custom_annotations vep_custom_annotations->detect_variants vep_custom_annotations normal_sequence normal_sequence: WT sequencing data and readgroup information normal_sequence->normal_alignment_and_qc sequence varscan_max_normal_freq varscan_max_normal_freq varscan_max_normal_freq->detect_variants varscan_max_normal_freq normal_name normal_name: String specifying the name of the WT sample normal_name->normal_alignment_and_qc final_name bqsr_known_sites bqsr_known_sites: One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. bqsr_known_sites->tumor_alignment_and_qc bqsr_known_sites bqsr_known_sites->normal_alignment_and_qc bqsr_known_sites target_interval_padding target_interval_padding: number of bp flanking each target region in which to allow variant calls target_interval_padding->pad_target_intervals roi_padding 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 qc_minimum_mapping_quality qc_minimum_mapping_quality qc_minimum_mapping_quality->tumor_alignment_and_qc qc_minimum_mapping_quality qc_minimum_mapping_quality->normal_alignment_and_qc qc_minimum_mapping_quality varscan_min_coverage varscan_min_coverage varscan_min_coverage->detect_variants varscan_min_coverage manta_output_contigs manta_output_contigs manta_output_contigs->manta output_contigs docm_vcf docm_vcf docm_vcf->detect_variants docm_vcf cle_vcf_filter cle_vcf_filter cle_vcf_filter->detect_variants cle_vcf_filter synonyms_file synonyms_file synonyms_file->detect_variants synonyms_file annotate_coding_only annotate_coding_only annotate_coding_only->detect_variants annotate_coding_only filter_somatic_llr_tumor_purity filter_somatic_llr_tumor_purity filter_somatic_llr_tumor_purity->detect_variants filter_somatic_llr_tumor_purity manta_non_wgs manta_non_wgs manta_non_wgs->manta non_wgs cnvkit_target_average_size cnvkit_target_average_size cnvkit_target_average_size->cnvkit cnvkit_target_average_size mutect_max_alt_alleles_in_normal_count mutect_max_alt_alleles_in_normal_count varscan_p_value varscan_p_value varscan_p_value->detect_variants varscan_p_value vep_to_table_fields vep_to_table_fields vep_to_table_fields->detect_variants vep_to_table_fields normal_sample_name normal_sample_name normal_sample_name->detect_variants normal_sample_name mutect_max_alt_allele_in_normal_fraction mutect_max_alt_allele_in_normal_fraction tumor_name tumor_name: String specifying the name of the MT sample tumor_name->tumor_alignment_and_qc final_name mutect_artifact_detection_mode mutect_artifact_detection_mode tumor_summary_hs_metrics tumor_summary_hs_metrics docm_filtered_vcf docm_filtered_vcf normal_snv_bam_readcount_tsv normal_snv_bam_readcount_tsv final_tsv final_tsv normal_summary_hs_metrics normal_summary_hs_metrics varscan_unfiltered_vcf varscan_unfiltered_vcf mutect_unfiltered_vcf mutect_unfiltered_vcf tumor_antitarget_coverage tumor_antitarget_coverage tumor_segmented_ratios tumor_segmented_ratios normal_per_base_coverage_metrics normal_per_base_coverage_metrics tumor_mark_duplicates_metrics tumor_mark_duplicates_metrics tumor_cram tumor_cram intervals_antitarget intervals_antitarget normal_hs_metrics normal_hs_metrics normal_antitarget_coverage normal_antitarget_coverage somatic_variants somatic_variants somalier_concordance_metrics somalier_concordance_metrics tumor_hs_metrics tumor_hs_metrics mutect_filtered_vcf mutect_filtered_vcf tumor_alignment_summary_metrics tumor_alignment_summary_metrics normal_cram normal_cram tumor_flagstats tumor_flagstats intervals_target intervals_target normal_mark_duplicates_metrics normal_mark_duplicates_metrics tumor_target_coverage tumor_target_coverage normal_verify_bam_id_metrics normal_verify_bam_id_metrics tumor_bin_level_ratios tumor_bin_level_ratios cn_diagram cn_diagram strelka_filtered_vcf strelka_filtered_vcf all_candidates all_candidates somalier_concordance_statistics somalier_concordance_statistics tumor_verify_bam_id_metrics tumor_verify_bam_id_metrics reference_coverage reference_coverage normal_per_target_coverage_metrics normal_per_target_coverage_metrics tumor_verify_bam_id_depth tumor_verify_bam_id_depth tumor_indel_bam_readcount_tsv tumor_indel_bam_readcount_tsv vep_summary vep_summary tumor_insert_size_metrics tumor_insert_size_metrics tumor_per_target_coverage_metrics tumor_per_target_coverage_metrics final_vcf final_vcf normal_flagstats normal_flagstats normal_verify_bam_id_depth normal_verify_bam_id_depth pindel_filtered_vcf pindel_filtered_vcf tumor_only_variants tumor_only_variants normal_target_coverage normal_target_coverage varscan_filtered_vcf varscan_filtered_vcf normal_insert_size_metrics normal_insert_size_metrics cn_scatter_plot cn_scatter_plot final_filtered_vcf final_filtered_vcf tumor_per_target_hs_metrics tumor_per_target_hs_metrics diploid_variants diploid_variants tumor_per_base_coverage_metrics tumor_per_base_coverage_metrics normal_indel_bam_readcount_tsv normal_indel_bam_readcount_tsv tumor_per_base_hs_metrics tumor_per_base_hs_metrics normal_per_target_hs_metrics normal_per_target_hs_metrics pindel_unfiltered_vcf pindel_unfiltered_vcf normal_per_base_hs_metrics normal_per_base_hs_metrics tumor_snv_bam_readcount_tsv tumor_snv_bam_readcount_tsv normal_alignment_summary_metrics normal_alignment_summary_metrics small_candidates small_candidates strelka_unfiltered_vcf strelka_unfiltered_vcf tumor_alignment_and_qc->tumor_summary_hs_metrics tumor_alignment_and_qc->tumor_mark_duplicates_metrics tumor_alignment_and_qc->tumor_hs_metrics tumor_alignment_and_qc->tumor_alignment_summary_metrics tumor_alignment_and_qc->tumor_flagstats tumor_alignment_and_qc->tumor_verify_bam_id_metrics tumor_alignment_and_qc->tumor_verify_bam_id_depth tumor_alignment_and_qc->tumor_insert_size_metrics tumor_alignment_and_qc->tumor_per_target_coverage_metrics tumor_alignment_and_qc->tumor_per_target_hs_metrics tumor_alignment_and_qc->tumor_per_base_coverage_metrics tumor_alignment_and_qc->tumor_per_base_hs_metrics tumor_alignment_and_qc->cnvkit tumor_bam tumor_alignment_and_qc->manta tumor_bam tumor_alignment_and_qc->concordance bam_1 tumor_alignment_and_qc->detect_variants tumor_bam tumor_alignment_and_qc->tumor_bam_to_cram bam normal_alignment_and_qc->normal_summary_hs_metrics normal_alignment_and_qc->normal_per_base_coverage_metrics normal_alignment_and_qc->normal_hs_metrics normal_alignment_and_qc->normal_mark_duplicates_metrics normal_alignment_and_qc->normal_verify_bam_id_metrics normal_alignment_and_qc->normal_per_target_coverage_metrics normal_alignment_and_qc->normal_flagstats normal_alignment_and_qc->normal_verify_bam_id_depth normal_alignment_and_qc->normal_insert_size_metrics normal_alignment_and_qc->normal_per_target_hs_metrics normal_alignment_and_qc->normal_per_base_hs_metrics normal_alignment_and_qc->normal_alignment_summary_metrics normal_alignment_and_qc->cnvkit reference normal_alignment_and_qc->manta normal_bam normal_alignment_and_qc->concordance bam_2 normal_alignment_and_qc->detect_variants normal_bam normal_alignment_and_qc->normal_bam_to_cram bam cnvkit->tumor_antitarget_coverage cnvkit->tumor_segmented_ratios cnvkit->intervals_antitarget cnvkit->normal_antitarget_coverage cnvkit->intervals_target cnvkit->tumor_target_coverage cnvkit->tumor_bin_level_ratios cnvkit->cn_diagram cnvkit->reference_coverage cnvkit->normal_target_coverage cnvkit->cn_scatter_plot manta->somatic_variants manta->all_candidates manta->tumor_only_variants manta->diploid_variants manta->small_candidates normal_index_cram samtools index cram normal_index_cram->normal_cram concordance->somalier_concordance_metrics concordance->somalier_concordance_statistics tumor_index_cram samtools index cram tumor_index_cram->tumor_cram detect_variants->docm_filtered_vcf detect_variants->normal_snv_bam_readcount_tsv detect_variants->final_tsv detect_variants->varscan_unfiltered_vcf detect_variants->mutect_unfiltered_vcf detect_variants->mutect_filtered_vcf detect_variants->strelka_filtered_vcf detect_variants->tumor_indel_bam_readcount_tsv detect_variants->vep_summary detect_variants->final_vcf detect_variants->pindel_filtered_vcf detect_variants->varscan_filtered_vcf detect_variants->final_filtered_vcf detect_variants->normal_indel_bam_readcount_tsv detect_variants->pindel_unfiltered_vcf detect_variants->tumor_snv_bam_readcount_tsv detect_variants->strelka_unfiltered_vcf pad_target_intervals->detect_variants roi_intervals normal_bam_to_cram->normal_index_cram cram tumor_bam_to_cram->tumor_index_cram cram default1 true default1->detect_variants strelka_exome_mode
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Inputs

ID Type Title Doc
docm_vcf File

The set of alleles that gatk haplotype caller will use to force-call regardless of evidence

omni_vcf File
trimming https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/trimming_options.yml#trimming_options (Optional)
vep_pick

configures how vep will annotate genomic features that each variant overlaps; for a detailed description of each option see https://useast.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick_allele_gene_eg

reference File reference: Reference fasta file for a desired assembly

reference contains the nucleotide sequence for a given assembly (hg37, hg38, etc.) in fasta format for the entire genome. This is what reads will be aligned to. Appropriate files can be found on ensembl at https://ensembl.org/info/data/ftp/index.html When providing the reference secondary files corresponding to reference indices must be located in the same directory as the reference itself. These files can be created with samtools index, bwa index, and picard CreateSequenceDictionary.

tumor_name String (Optional) tumor_name: String specifying the name of the MT sample

tumor_name provides a string for what the MT sample will be referred to in the various outputs, for example the VCF files.

normal_name String (Optional) normal_name: String specifying the name of the WT sample

normal_name provides a string for what the WT sample will be referred to in the various outputs, for example the VCF files.

somalier_vcf File

a vcf file of known polymorphic sites for somalier to compare normal and tumor samples for identity; sites files can be found at: https://github.com/brentp/somalier/releases

manta_non_wgs Boolean (Optional)

toggles on or off manta settings for WES vs. WGS mode for structural variant detection

scatter_count Integer

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

synonyms_file File (Optional)

synonyms_file allows the use of different chromosome identifiers in vep inputs or annotation files (cache, database, GFF, custom file, fasta). File should be tab-delimited with the primary identifier in column 1 and the synonym in column 2.

vep_cache_dir Directory

path to the vep cache directory, available at: https://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html#pre

bait_intervals File bait_intervals: interval_list file of baits used in the sequencing experiment

bait_intervals is an interval_list corresponding to the baits used in sequencing reagent. These are essentially coordinates for regions you were able to design probes for in the reagent. Typically the reagent provider has this information available in bed format and it can be converted to an interval_list with Picard BedToIntervalList. Astrazeneca also maintains a repo of baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data

bqsr_intervals String[] bqsr_intervals: Array of strings specifying regions for base quality score recalibration

bqsr_intervals provides an array of genomic intervals for which to apply GATK base quality score recalibrations. Typically intervals are given for the entire chromosome (chr1, chr2, etc.), these names should match the format in the reference file.

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.

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

Known polymorphic indels recommended by GATK for a variety of tools including the BaseRecalibrator. This is part of the GATK resource bundle available at http://www.broadinstitute.org/gatk/guide/article?id=1213 File should be in vcf format, and tabix indexed.

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
manta_call_regions File (Optional)

bgzip-compressed, tabix-indexed BED file specifiying regions to which manta structural variant analysis is limited

normal_sample_name String
per_base_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[] per_base_intervals: additional intervals over which to summarize coverage/QC at a per-base resolution

per_base_intervals is a list of regions (in interval_list format) over which to summarize coverage/QC at a per-base resolution.

pindel_insert_size Integer
validated_variants File (Optional)

An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF

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[]

VEP fields in final output

annotate_coding_only Boolean (Optional)

if set to true, vep only returns consequences that fall in the coding regions of transcripts

filter_docm_variants Boolean (Optional)
manta_output_contigs Boolean (Optional)

if set to true configures manta to output assembled contig sequences in the final VCF files

per_target_intervals https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/types/labelled_file.yml#labelled_file[] per_target_intervals: additional intervals over which to summarize coverage/QC at a per-target resolution

per_target_intervals list of regions (in interval_list format) over which to summarize coverage/QC at a per-target resolution.

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: number of bp flanking each target region in which to allow variant calls

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[]

The names of one or more standard VCF fields or INFO fields to include in the output table

cnvkit_target_average_size Integer (Optional)

approximate size of split target bins for CNVkit; if not set a suitable window size will be set by CNVkit automatically

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.

mutect_artifact_detection_mode Boolean
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[]

The name of a genotype field to include in the output table

mutect_max_alt_alleles_in_normal_count Integer (Optional)
mutect_max_alt_allele_in_normal_fraction Float (Optional)
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
manta
../tools/manta_somatic.cwl (CommandLineTool)
Set up and execute manta
cnvkit
../tools/cnvkit_batch.cwl (CommandLineTool)

Note: cnvkit batch is a complex command that is capable of running all or part of the cnvkit internal pipeline, depending on the combination of inputs provided to it. In order to take advantage of this, most inputs to this cwl are optional, so that different workflows can use different forms of the command while still using a single cwl file. For further reading, see the relevant cnvkit docs at https://cnvkit.readthedocs.io/en/stable/quickstart.html#build-a-reference-from-normal-samples-and-infer-tumor-copy-ratios https://cnvkit.readthedocs.io/en/stable/pipeline.html#batch In our pipelines, the command form is mainly determined by the components of the reference input. The somatic_exome cwl pipeline provides a fasta file and a normal bam, which causes the batch pipeline to construct a copy number reference (.cnn file) based on the normal bam. The germline_wgs cwl pipeline does not provide a normal bam; instead it passes a cnn reference file as an optional input. This file is intended to be manually generated from a reference normal sample for use in the pipeline. If it is not provided, cnvkit will automatically generate a flat reference file.

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

Outputs

ID Type Label Doc
final_tsv File
final_vcf File
cn_diagram File (Optional)
tumor_cram File
normal_cram File
vep_summary File
all_candidates File
cn_scatter_plot File (Optional)
tumor_flagstats File
diploid_variants File (Optional)
intervals_target File (Optional)
normal_flagstats File
small_candidates File
somatic_variants File (Optional)
tumor_hs_metrics File
docm_filtered_vcf File
normal_hs_metrics File
final_filtered_vcf File
reference_coverage File (Optional)
mutect_filtered_vcf File
pindel_filtered_vcf File
tumor_only_variants File (Optional)
intervals_antitarget File (Optional)
strelka_filtered_vcf File
varscan_filtered_vcf File
mutect_unfiltered_vcf File
pindel_unfiltered_vcf File
tumor_target_coverage File
normal_target_coverage File
strelka_unfiltered_vcf File
tumor_bin_level_ratios File
tumor_segmented_ratios File
varscan_unfiltered_vcf File
tumor_summary_hs_metrics File[]
normal_summary_hs_metrics File[]
tumor_antitarget_coverage File
tumor_insert_size_metrics File
tumor_per_base_hs_metrics File[]
tumor_verify_bam_id_depth File
normal_antitarget_coverage 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.cwl