Workflow: Apply filters to VCF file
Fetched 2023-01-11 12:53:53 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 |
|---|---|---|---|
| vcf | File | ||
| reference | String | ||
| tumor_bam | File | ||
| do_cle_vcf_filter | Boolean | ||
| filter_mapq0_threshold | Float | ||
| filter_gnomADe_maximum_population_allele_frequency | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter_vcf_cle |
../definitions/tools/filter_vcf_cle.cwl
(CommandLineTool)
|
cle_annotated_vcf_filter | |
| filter_vcf_mapq0 |
../definitions/tools/filter_vcf_mapq0.cwl
(CommandLineTool)
|
filter_vcf for variants with high percentage of mapq0 reads | |
| filter_vcf_gnomADe_allele_freq |
../definitions/tools/filter_vcf_gnomADe_allele_freq.cwl
(CommandLineTool)
|
gnomADe_AF filter |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/3e84098f77686523fe3dbb807b35450b56501c59/detect_variants/filter_vcf.cwl
