Workflow: Filter single sample sv vcf from paired read callers(Manta/Smoove)
Fetched 2025-01-16 18:01:38 GMT
Verified with cwltool version 3.1.20230201224320
- 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 |
|---|---|---|---|
| bam | File | ||
| sv_vcf | File | ||
| snps_vcf | File (Optional) | ||
| reference | File | ||
| vcf_source | |||
| deletion_depth | Double (Optional) | ||
| sv_split_count | Integer (Optional) | ||
| output_vcf_name | String (Optional) | ||
| sv_paired_count | Integer (Optional) | ||
| duplication_depth | Double (Optional) | ||
| abundance_percentage | Double (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| depth_filter |
../tools/filter_sv_vcf_depth.cwl
(CommandLineTool)
|
||
| duphold_annotate |
../tools/duphold.cwl
(CommandLineTool)
|
||
| filtered_vcf_bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| filtered_vcf_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| read_support_filter |
../tools/filter_sv_vcf_read_support.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/5fda2d9eb52a363bd51011b3851c2afb86318c0c/definitions/subworkflows/sv_paired_read_caller_filter.cwl
