Workflow: scatter GATK HaplotypeCaller over intervals
Fetched 2023-01-14 15:18:52 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
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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 | 4e35ee9e11703caafdb0911ae0ed2402[] | ||
| reference | File | ||
| read_filter | String (Optional) | ||
| gvcf_gq_bands | String[] | ||
| output_prefix | String (Optional) |
an optional string to prepend to the output filename |
|
| variant_index_type | |||
| max_alternate_alleles | Integer (Optional) | ||
| contamination_fraction | String (Optional) | ||
| variant_index_parameter | String (Optional) | ||
| emit_reference_confidence |
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/9161ef43f7bf0e22b365fde9ec92edcb8601798e/definitions/subworkflows/gatk_haplotypecaller_iterator.cwl
