Workflow: exomeseq-gatk4/v2.2.0
Fetched 2024-05-18 23:55:07 GMT
Verified with cwltool version 3.1.20221201130942
Whole Exome Sequence analysis using GATK4 - v2.2.0
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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 |
|---|---|---|---|
| library | String | ||
| threads | Integer | ||
| platform | String | ||
| read_pairs | https://w3id.org/cwl/view/git/fd641e00364e257b2119ce5b26aedb01402dfcbe/types/FASTQReadPairType.yml#FASTQReadPairType[] | ||
| study_type | https://w3id.org/cwl/view/git/fd641e00364e257b2119ce5b26aedb01402dfcbe/types/ExomeseqStudyType.yml#ExomeseqStudyType | ||
| known_sites | File[] | ||
| bait_intervals | File[] (Optional) | ||
| resource_dbsnp | File | ||
| interval_padding | Integer (Optional) | ||
| reference_genome | File | ||
| snp_resource_1kg | File | ||
| target_intervals | File[] (Optional) | ||
| snp_resource_omni | File | ||
| snp_resource_hapmap | File | ||
| indel_resource_mills | File | ||
| variant_recalibration_annotations_snps | String[] | ||
| variant_recalibration_annotations_indels | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| preprocessing | |||
| variant_discovery | |||
| organize_directories | |||
| prepare_reference_data |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| raw_variants_dir | Directory | ||
| joint_raw_variants | File |
GVCF file from joint genotyping calling |
|
| bams_recalibrated_dir | Directory |
BAM files containing recalibrated reads |
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| fastp_html_reports_dir | Directory | ||
| fastp_json_reports_dir | Directory | ||
| bams_markduplicates_dir | Directory |
BAM and bai files from markduplicates |
|
| markduplicates_metrics_dir | Directory |
metrics files from markduplicates |
|
| filtered_recalibrated_variants | File |
The output filtered and recalibrated VCF file in which each variant is annotated with its VQSLOD value |
|
| variant_calling_detail_metrics | File | ||
| variant_calling_summary_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/fd641e00364e257b2119ce5b26aedb01402dfcbe/exomeseq-gatk4.cwl
