Workflow: scatter GATK HaplotypeCaller over intervals
Fetched 2023-01-13 17:56:14 GMT
Verified with cwltool version 3.1.20221201130942
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- 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 | ||
| dbsnp_vcf | File (Optional) | ||
| intervals | a8f1ddc076c24739045c647590fd5e18[] | ||
| reference | String | ||
| gvcf_gq_bands | String[] | ||
| contamination_fraction | String (Optional) | ||
| emit_reference_confidence | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| haplotype_caller |
../tools/gatk_haplotype_caller.cwl
(CommandLineTool)
|
GATK HaplotypeCaller |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gvcf | File[] |
Permalink:
https://w3id.org/cwl/view/git/a670f323e77e02d9b77be9a13d73d5276dd3676c/definitions/subworkflows/gatk_haplotypecaller_iterator.cwl
