Workflow: Whole Exome Sequencing
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/ef08cb00bd55b4c712645d171dbc691e01ed6165/packed/exomeseq.cwl#bespin-types.yml/NamedFASTQFilePairType[] | ||
study_type | https://w3id.org/cwl/view/git/ef08cb00bd55b4c712645d171dbc691e01ed6165/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/ef08cb00bd55b4c712645d171dbc691e01ed6165/packed/exomeseq.cwl?part=main