pipelines_detect_variants_wgs.cwl
APipe Tester edited this page Mar 3, 2022
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Detect Variants workflow for WGS pipeline
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| reference | string | |||
| tumor_bam | File | ['.bai', '^.bai'] | ||
| normal_bam | File | ['.bai', '^.bai'] | ||
| roi_intervals | File | |||
| strelka_exome_mode | boolean | |||
| strelka_cpu_reserved | int? | |||
| readcount_minimum_base_quality | int? | |||
| readcount_minimum_mapping_quality | int? | |||
| scatter_count | scatters each supported variant detector (varscan, mutect) into this many parallel jobs | int? | ||
| varscan_strand_filter | int? | |||
| varscan_min_coverage | int? | |||
| varscan_min_var_freq | float? | |||
| varscan_p_value | float? | |||
| varscan_max_normal_freq | float? | |||
| docm_vcf | File | ['.tbi'] | ||
| filter_docm_variants | boolean? | |||
| vep_cache_dir | ['string', 'Directory'] | |||
| vep_ensembl_assembly | genome assembly to use in vep. Examples: GRCh38 or GRCm38 | string | ||
| vep_ensembl_version | ensembl version - Must be present in the cache directory. Example: 95 | string | ||
| vep_ensembl_species | ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus | string | ||
| synonyms_file | File? | |||
| annotate_coding_only | boolean? | |||
| vep_pick | ['null', {'type': 'enum', 'symbols': ['pick', 'flag_pick', 'pick_allele', 'per_gene', 'pick_allele_gene', 'flag_pick_allele', 'flag_pick_allele_gene']}] | |||
| vep_plugins | string[]? | |||
| filter_gnomADe_maximum_population_allele_frequency | float? | |||
| filter_mapq0_threshold | float? | |||
| filter_minimum_depth | int? | |||
| filter_somatic_llr_threshold | 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. | float | ||
| filter_somatic_llr_tumor_purity | 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 | float | ||
| filter_somatic_llr_normal_contamination_rate | 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 | float | ||
| cle_vcf_filter | boolean? | |||
| variants_to_table_fields | string[]? | |||
| variants_to_table_genotype_fields | string[]? | |||
| vep_to_table_fields | string[]? | |||
| tumor_sample_name | string | |||
| normal_sample_name | string | |||
| vep_custom_annotations | custom type, check types directory for input format | ../types/vep_custom_annotation.yml#vep_custom_annotation[] | ||
| validated_variants | An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF | File? | ['.tbi'] |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| mutect_unfiltered_vcf | File | ['.tbi'] | ||
| mutect_filtered_vcf | File | ['.tbi'] | ||
| strelka_unfiltered_vcf | File | ['.tbi'] | ||
| strelka_filtered_vcf | File | ['.tbi'] | ||
| varscan_unfiltered_vcf | File | ['.tbi'] | ||
| varscan_filtered_vcf | File | ['.tbi'] | ||
| docm_filtered_vcf | File | ['.tbi'] | ||
| final_vcf | File | ['.tbi'] | ||
| final_filtered_vcf | File | ['.tbi'] | ||
| final_tsv | File | |||
| vep_summary | File | |||
| tumor_snv_bam_readcount_tsv | File | |||
| tumor_indel_bam_readcount_tsv | File | |||
| normal_snv_bam_readcount_tsv | File | |||
| normal_indel_bam_readcount_tsv | File |
| Name | CWL Run |
|---|---|
| mutect | subworkflows/mutect.cwl |
| strelka | subworkflows/strelka_and_post_processing.cwl |
| varscan | subworkflows/varscan_pre_and_post_processing.cwl |
| docm | subworkflows/docm_cle.cwl |
| combine | tools/combine_variants_wgs.cwl |
| add_docm_variants | tools/docm_add_variants.cwl |
| decompose | tools/vt_decompose.cwl |
| decompose_index | tools/index_vcf.cwl |
| annotate_variants | tools/vep.cwl |
| tumor_bam_readcount | tools/bam_readcount.cwl |
| normal_bam_readcount | tools/bam_readcount.cwl |
| add_tumor_bam_readcount_to_vcf | subworkflows/vcf_readcount_annotator.cwl |
| add_normal_bam_readcount_to_vcf | subworkflows/vcf_readcount_annotator.cwl |
| index | tools/index_vcf.cwl |
| filter_vcf | subworkflows/filter_vcf.cwl |
| annotated_filter_bgzip | tools/bgzip.cwl |
| annotated_filter_index | tools/index_vcf.cwl |
| variants_to_table | tools/variants_to_table.cwl |
| add_vep_fields_to_table | tools/add_vep_fields_to_table.cwl |