Workflow: Unaligned BAM to BQSR and VCF
Fetched 2023-01-04 21:14:51 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:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bams | File[] | ||
| reference | String | ||
| readgroups | String[] | ||
| bqsr_known_sites | File[] |
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bqsr |
../tools/bqsr.cwl
(CommandLineTool)
|
create BQSR table | |
| align |
align.cwl
(Workflow)
|
Unaligned to aligned BAM | |
| merge |
../tools/merge_bams.cwl
(CommandLineTool)
|
Sambamba: merge | |
| index_bam |
../tools/index_bam.cwl
(CommandLineTool)
|
samtools index | |
| apply_bqsr |
../tools/apply_bqsr.cwl
(CommandLineTool)
|
apply BQSR | |
| index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| position_sort |
../tools/position_sort.cwl
(CommandLineTool)
|
sort BAM by position |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_cram | File |
Permalink:
https://w3id.org/cwl/view/git/509938802c5e42bb8084c6a5a26ab6425c60e69a/definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl
