Workflow: exome alignment and germline variant detection
Fetched 2026-10-09 21:14:46 GMT
Verified with cwltool version 3.1.20230201224320
- 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[] | ||
| dbsnp | File | ||
| mills | File | ||
| omni_vcf | File | ||
| intervals | 8b208225bdc63d38fe72f11c745dfbd0[] | ||
| reference | String | ||
| readgroups | String[] | ||
| known_indels | File | ||
| gvcf_gq_bands | String[] | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] (Optional) | ||
| target_intervals | File | ||
| emit_reference_confidence | String | ||
| picard_metric_accumulation_level | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| extract_freemix |
germline_exome_workflow.cwl#extract_freemix/e5932e06-2c2d-4395-b69b-9e1665728a03
(ExpressionTool)
|
||
| alignment_and_qc |
exome_alignment.cwl
(Workflow)
|
exome alignment with qc | |
| haplotype_caller | scatter GATK HaplotypeCaller over intervals |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| gvcf | File[] | ||
| flagstats | File | ||
| hs_metrics | File | ||
| insert_size_metrics | File | ||
| verify_bam_id_depth | File | ||
| verify_bam_id_metrics | File | ||
| mark_duplicates_metrics | File | ||
| alignment_summary_metrics | File | ||
| per_base_coverage_metrics | File (Optional) | ||
| per_target_coverage_metrics | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/8f21f80a504c7fb834af331715a0661707d25537/germline_exome_workflow.cwl
