Workflow: scatter GATK HaplotypeCaller over intervals
Fetched 2023-01-12 16:40:54 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 | c3b49063277a6f890af033ed3ae4abfb[] | ||
| 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/0798b3933ae3e6486596294984c7ffee50b94ef5/definitions/subworkflows/gatk_haplotypecaller_iterator.cwl
