Workflow: wgs alignment and germline variant detection
Fetched 2025-08-23 05:26:18 GMT
Verified with cwltool version 3.1.20230201224320
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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[] | ||
| mills | File | ||
| omni_vcf | File | ||
| dbsnp_vcf | File | ||
| intervals | 9a5135945a4a344d7cc18a50f09cbb15[] | ||
| reference | String | ||
| readgroups | String[] | ||
| coding_only | Boolean (Optional) | ||
| known_indels | File | ||
| qc_intervals | File | ||
| gvcf_gq_bands | String[] | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String (Optional) | ||
| hgvs_annotation | Boolean (Optional) | ||
| custom_gnomad_vcf | File (Optional) | ||
| emit_reference_confidence | String | ||
| variant_reporting_intervals | File | ||
| picard_metric_accumulation_level | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| detect_variants |
../subworkflows/germline_detect_variants.cwl
(Workflow)
|
exome alignment and germline variant detection | |
| extract_freemix |
germline_wgs.cwl#extract_freemix/dc267bf1-d4be-4d74-818d-5a2017788053
(ExpressionTool)
|
||
| alignment_and_qc |
wgs_alignment.cwl
(Workflow)
|
wgs alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| gvcf | File[] | ||
| final_vcf | File | ||
| flagstats | File | ||
| coding_vcf | File | ||
| limited_vcf | File | ||
| vep_summary | File | ||
| wgs_metrics | File | ||
| gc_bias_metrics | File | ||
| insert_size_metrics | File | ||
| verify_bam_id_depth | File | ||
| gc_bias_metrics_chart | File | ||
| insert_size_histogram | File | ||
| verify_bam_id_metrics | File | ||
| gc_bias_metrics_summary | File | ||
| mark_duplicates_metrics | File | ||
| alignment_summary_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/293dc7b83639d21a56efff2baf9dfe4e97b9b806/definitions/pipelines/germline_wgs.cwl
