Workflow: Whole genome alignment and somatic variant detection
Fetched 2023-01-09 17:40:06 GMT
Verified with cwltool version 3.1.20221201130942
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- Default Values
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- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| docm_vcf | File | ||
| omni_vcf | File | ||
| trimming | https://w3id.org/cwl/view/git/25eab0390f6866ce491b44c89d9e0435d228ab6f/definitions/types/trimming_options.yml#trimming_options (Optional) | ||
| vep_pick | |||
| reference | String | ||
| tumor_name | String (Optional) | ||
| normal_name | String (Optional) | ||
| qc_intervals | File | ||
| somalier_vcf | File | ||
| manta_non_wgs | Boolean (Optional) | ||
| scatter_count | Integer |
scatters each supported variant detector (varscan, mutect) into this many parallel jobs |
|
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| tumor_sequence | https://w3id.org/cwl/view/git/25eab0390f6866ce491b44c89d9e0435d228ab6f/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/25eab0390f6866ce491b44c89d9e0435d228ab6f/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 | ||
| summary_intervals | https://w3id.org/cwl/view/git/25eab0390f6866ce491b44c89d9e0435d228ab6f/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| manta_call_regions | File (Optional) | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/25eab0390f6866ce491b44c89d9e0435d228ab6f/definitions/types/labelled_file.yml#labelled_file[] | ||
| 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[] | ||
| annotate_coding_only | Boolean (Optional) | ||
| filter_docm_variants | Boolean (Optional) | ||
| manta_output_contigs | Boolean (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/25eab0390f6866ce491b44c89d9e0435d228ab6f/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/25eab0390f6866ce491b44c89d9e0435d228ab6f/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| 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[] | ||
| 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_wgs.cwl
(Workflow)
|
Detect Variants workflow for WGS pipeline | |
| 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 | |
| tumor_alignment_and_qc |
alignment_wgs.cwl
(Workflow)
|
wgs alignment with qc | |
| normal_alignment_and_qc |
alignment_wgs.cwl
(Workflow)
|
wgs alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| tumor_cram | File | ||
| normal_cram | File | ||
| vep_summary | File | ||
| all_candidates | File | ||
| tumor_flagstats | File | ||
| diploid_variants | File (Optional) | ||
| normal_flagstats | File | ||
| small_candidates | File | ||
| somatic_variants | File (Optional) | ||
| docm_filtered_vcf | File | ||
| tumor_wgs_metrics | File | ||
| final_filtered_vcf | File | ||
| normal_wgs_metrics | File | ||
| mutect_filtered_vcf | File | ||
| tumor_only_variants | File (Optional) | ||
| strelka_filtered_vcf | File | ||
| varscan_filtered_vcf | File | ||
| mutect_unfiltered_vcf | File | ||
| tumor_gc_bias_metrics | File | ||
| normal_gc_bias_metrics | 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_gc_bias_metrics_chart | File | ||
| tumor_insert_size_histogram | File | ||
| tumor_per_target_hs_metrics | File[] | ||
| tumor_snv_bam_readcount_tsv | File | ||
| tumor_verify_bam_id_metrics | File | ||
| normal_gc_bias_metrics_chart | File | ||
| normal_insert_size_histogram | File | ||
| normal_per_target_hs_metrics | File[] | ||
| normal_snv_bam_readcount_tsv | File | ||
| normal_verify_bam_id_metrics | File | ||
| somalier_concordance_metrics | File | ||
| tumor_gc_bias_metrics_summary | File | ||
| tumor_indel_bam_readcount_tsv | File | ||
| tumor_mark_duplicates_metrics | File | ||
| normal_gc_bias_metrics_summary | 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[] |
https://w3id.org/cwl/view/git/25eab0390f6866ce491b44c89d9e0435d228ab6f/definitions/pipelines/somatic_wgs.cwl
