Workflow: Filter single sample sv vcf from depth callers(cnvkit/cnvnator)
- 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 |
---|---|---|---|
sv_vcf | File | ||
vcf_source | |||
min_sv_size | Integer (Optional) | ||
deletion_depth | Double (Optional) | ||
output_vcf_name | String (Optional) | ||
duplication_depth | Double (Optional) |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
size_filter |
../tools/filter_sv_vcf_size.cwl
(CommandLineTool)
|
||
depth_filter |
../tools/filter_sv_vcf_depth.cwl
(CommandLineTool)
|
||
filtered_vcf_bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
filtered_vcf_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
filtered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a/definitions/subworkflows/sv_depth_caller_filter.cwl