Workflow: Scattered variant calling workflow
Fetched 2024-11-24 15:19:09 GMT
Verified with cwltool version 3.1.20230201224320
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- Default Values
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
GNU Affero General Public License v3.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File [BAM] | Indexed sorted BAM with labeled duplicates | |
| sample | String | Sample Name | |
| reference | File [FASTA] | Reference genome | |
| knownsites1 | File [VCF] | VCF of known SNPS sites for BQSR | |
| knownsites2 | File [VCF] | VCF of known indel sites for BQSR | |
| scattercount | String | Desired split for variant calling | |
| fullintervallist | File | Full list of intervals to operate over |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gather-GVCFs |
gather-array-vcf.cwl
(CommandLineTool)
|
Gather GVCFs | |
| splitintervals |
gatk-splitintervals.cwl
(CommandLineTool)
|
Create scatter interval files | |
| recal-haplotypecaller |
gatk-wf-with-interval.cwl
(Workflow)
|
Variant calling workflow for given interval |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gatheredgvcf | File [VCF] | Gathered GVCF |
Permalink:
https://w3id.org/cwl/view/git/e4d896f5f94a9cf7b157cf87d5042e416649d87b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
