Workflow: SNV background error suppression using panel of normals
Fetched 2025-04-28 11:48:04 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
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- Inputs/Outputs
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source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| vcf | File | ||
| reference | File | ||
| roi_intervals | File | ||
| panel_of_normal_bams | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| prep |
../tools/prep_for_PoN.cwl
(CommandLineTool)
|
Prepare vcf for HaplotypeCaller (GATK) | |
| index |
../tools/gatk_IndexFeatureFile.cwl
(CommandLineTool)
|
Create VCF index using IndexFeatureFile (GATK) | |
| index2 |
../tools/gatk_IndexFeatureFile.cwl
(CommandLineTool)
|
Create VCF index using IndexFeatureFile (GATK) | |
| index3 |
../tools/gatk_IndexFeatureFile.cwl
(CommandLineTool)
|
Create VCF index using IndexFeatureFile (GATK) | |
| genotype_PoN |
../tools/gatk_haplotype_caller_PoN.cwl
(CommandLineTool)
|
HaplotypeCaller (GATK4) | |
| identify_noise |
../tools/identify_PoN_support.cwl
(CommandLineTool)
|
Create a VCF that contains onlys SNVs/INDELs supported by x% of the samples in a panel of normals | |
| suppress_noise |
../tools/gatk_VariantFiltration.cwl
(CommandLineTool)
|
Create VCF index using VariantFiltration (GATK) |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/656d9ae18f164f983c5672bcf51037cd73309f4f/subworkflows/suppress_background_error.cwl
