Workflow: Whole Exome Sequencing
Fetched 2025-11-04 06:58:26 GMT
Verified with cwltool version 3.1.20221201130942
Whole Exome Sequence analysis using GATK best practices - Germline SNP & Indel Discovery
- 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 |
|---|---|---|---|
| GATKJar | File | ||
| library | String | ||
| threads | Integer (Optional) | ||
| platform | String | ||
| intervals | File[] (Optional) | ||
| knownSites | File[] | ||
| read_pairs | https://w3id.org/cwl/view/git/e2dc95d4f12210359360d814382e7201d836dfcf/packed/exomeseq.cwl#bespin-types.yml/NamedFASTQFilePairType[] | ||
| study_type | https://w3id.org/cwl/view/git/e2dc95d4f12210359360d814382e7201d836dfcf/packed/exomeseq.cwl#bespin-types.yml/ExomeseqStudyType | ||
| resource_dbsnp | File | ||
| interval_padding | Integer (Optional) | ||
| reference_genome | File | ||
| snp_resource_1kg | File | ||
| primary_intervals | File[] (Optional) | ||
| snp_resource_omni | File | ||
| snp_resource_hapmap | File | ||
| indel_resource_mills | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| preprocessing |
exomeseq.cwl#exomeseq-01-preprocessing.cwl
(Workflow)
|
||
| variant_discovery | |||
| organize_directories | |||
| prepare_reference_data |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bams_final_dir | Directory |
BAM files containing assembled haplotypes and locally realigned reads |
|
| hs_metrics_dir | Directory | ||
| raw_variants_dir | Directory | ||
| trim_reports_dir | Directory | ||
| fastqc_reports_dir | Directory | ||
| joint_raw_variants | File |
GVCF file from joint genotyping calling |
|
| bams_markduplicates_dir | Directory |
BAM and bai files from markduplicates |
|
| filtered_recalibrated_variants | File |
The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value |
Permalink:
https://w3id.org/cwl/view/git/e2dc95d4f12210359360d814382e7201d836dfcf/packed/exomeseq.cwl?part=main
