Workflow: Apply filters to VCF file
Fetched 2025-12-14 14:02:12 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 |
|---|---|---|---|
| reference | File | ||
| annotated_vcf | File | ||
| gnomad_field_name | String | ||
| limit_variant_intervals | File | ||
| filter_gnomAD_maximum_population_allele_frequency | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| limit_variants |
../tools/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 4.1.8.1) | |
| bgzip_filtered_vcf |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| index_filtered_vcf |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| coding_variant_filter |
../tools/filter_vcf_coding_variant.cwl
(CommandLineTool)
|
Coding Variant filter | |
| set_filtered_vcf_name |
../tools/staged_rename.cwl
(CommandLineTool)
|
Staged Renamer |
Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead. |
| gnomad_frequency_filter |
../tools/filter_vcf_custom_allele_freq.cwl
(CommandLineTool)
|
Custom allele frequency filter |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_vcf | File | ||
| filtered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/5fda2d9eb52a363bd51011b3851c2afb86318c0c/definitions/subworkflows/germline_filter_vcf.cwl
