Workflow: Variant calling workflow for given interval
Fetched 2023-01-10 08:20:51 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 [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 | |
| intervallist | File | Scatter intervals 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)
|
Generate recalibration table for BQSR | |
| selectvariants |
gatk-selectvariants.cwl
(CommandLineTool)
|
Filter unused alternates | |
| haplotypecaller |
gatk-haplotypecaller-with-interval.cwl
(CommandLineTool)
|
Call variants with GATK HaplotypeCaller |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gvcf | File [VCF] | Given interval filtered GVCF |
Permalink:
https://w3id.org/cwl/view/git/d147d1d1fafeeea06bd09d9479337b0f5aab43b0/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
