Workflow: merge and annotate svs with population allele freq and vep
Fetched 2023-01-03 20:12:34 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| vcfs | File[] | ||
| sv_db | File | ||
| reference | String | ||
| same_type | Boolean | ||
| coding_only | Boolean (Optional) | ||
| cohort_name | String (Optional) | ||
| same_strand | Boolean | ||
| vep_plugins | String[] (Optional) | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String | ||
| minimum_sv_size | Integer | ||
| minimum_sv_calls | Integer | ||
| custom_gnomad_vcf | File (Optional) | ||
| custom_clinvar_vcf | File (Optional) | ||
| 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 |
|
| estimate_sv_distance | Boolean | ||
| vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
| max_distance_to_merge | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort_vcf |
../tools/sort_vcf.cwl
(CommandLineTool)
|
Sort VCF | |
| merge_vcfs |
../tools/survivor.cwl
(CommandLineTool)
|
Run SURVIVOR to merge SV calls | |
| annotate_variants |
../tools/vep.cwl
(CommandLineTool)
|
Ensembl Variant Effect Predictor | |
| add_population_frequency |
../tools/add_sv_population_frequency.cwl
(CommandLineTool)
|
add population allele frequencies to a vcf |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| vep_summary | File | ||
| merged_annotated_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/735be84cdea041fcc8bd8cbe5728b29ca3586a21/definitions/subworkflows/merge_svs.cwl
