Workflow: gatk-wf-with-interval.cwl
Fetched 2023-01-11 20:13:39 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
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)
|
Applying 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/36de0d12e1cc88d0fd7d6b401df6c6e403f8c809/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
