Workflow: gatk-wf-with-interval.cwl
Fetched 2023-01-04 01:13:09 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 | ||
| sample | String | ||
| reference | File | ||
| knownsites1 | File | ||
| intervallist | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| applyBQSR |
gatk-applyBSQR-with-interval.cwl
(CommandLineTool)
|
Apply base quality score recalibration | |
| basecalibrator |
gatk-baserecalibrator-with-interval.cwl
(CommandLineTool)
|
Generating recalibration table for BQSR | |
| selectvariants |
gatk-selectvariants.cwl
(CommandLineTool)
|
||
| haplotypecaller |
gatk-haplotypecaller-with-interval.cwl
(CommandLineTool)
|
Germline variant calling using GATK with output gvcf |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gvcf | File |
Permalink:
https://w3id.org/cwl/view/git/b50ffeeeae865d0780ca03c5a3f5065eeeb758e4/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
