Workflow: exomeseq-gatk4-02-variantdiscovery.cwl
Fetched 2024-05-03 11:31:51 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| name | String | ||
| intervals | File[] (Optional) | ||
| study_type | https://w3id.org/cwl/view/git/f07a07037e7c162f117b3706614d885741a44518/types/ExomeseqStudyType.yml#ExomeseqStudyType | ||
| raw_variants | File[] | ||
| resource_dbsnp | File | ||
| interval_padding | Integer (Optional) | ||
| reference_genome | File | ||
| snp_resource_1kg | File | ||
| snp_resource_omni | File | ||
| snp_resource_hapmap | File | ||
| indel_resource_mills | File | ||
| target_interval_list | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| apply_vqsr_snps |
../tools/GATK4/GATK4-ApplyVQSR.cwl
(CommandLineTool)
|
||
| collect_metrics |
../tools/GATK4/GATK4-CollectVariantCallingMetrics.cwl
(CommandLineTool)
|
||
| combine_variants |
../tools/GATK4/GATK4-CombineGVCFs.cwl
(CommandLineTool)
|
||
| joint_genotyping |
../tools/GATK4/GATK4-GenotypeGVCFs.cwl
(CommandLineTool)
|
||
| apply_vqsr_indels |
../tools/GATK4/GATK4-ApplyVQSR.cwl
(CommandLineTool)
|
||
| extract_sequence_dict |
../utils/extract-secondary-file.cwl
(ExpressionTool)
|
||
| generate_joint_filenames |
../utils/generate-joint-filenames-gatk4.cwl
(ExpressionTool)
|
Generates a set of file names for joint steps based on an input name | |
| generate_annotations_snps |
../utils/generate-variant-recalibration-annotation-set.cwl
(ExpressionTool)
|
Given an ExomeseqStudyType returns an array of the annotations to use. |
The InbreedingCoeff is a population level statistic that requires at least 10 samples in order to be computed. For projects with fewer samples, or that includes many closely related samples (such as a family) please omit this annotation from the command line. From https://software.broadinstitute.org/gatk/documentation/article?id=1259 |
| variant_recalibration_snps |
../tools/GATK4/GATK4-VariantRecalibrator-SNPs.cwl
(CommandLineTool)
|
||
| generate_annotations_indels |
../utils/generate-variant-recalibration-annotation-set.cwl
(ExpressionTool)
|
Given an ExomeseqStudyType returns an array of the annotations to use. |
The InbreedingCoeff is a population level statistic that requires at least 10 samples in order to be computed. For projects with fewer samples, or that includes many closely related samples (such as a family) please omit this annotation from the command line. From https://software.broadinstitute.org/gatk/documentation/article?id=1259 |
| variant_recalibration_indels |
../tools/GATK4/GATK4-VariantRecalibrator-Indels.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| detail_metrics | File | ||
| summary_metrics | File | ||
| joint_raw_variants | File |
VCF file from joint genotyping calling |
|
| variant_recalibration_indels_vcf | File |
The output VCF file after INDEL recalibration |
|
| variant_recalibration_combined_vcf | File |
The output VCF file after INDEL and SNP recalibration |
|
| variant_recalibration_snps_tranches | File |
The output tranches file used by ApplyVQSR in SNP mode |
|
| variant_recalibration_indels_tranches | File |
The output tranches file used by ApplyVQSR in INDEL mode |
|
| variant_recalibration_snps_recalibration | File |
The output recalibration file used by ApplyVQSR in SNP mode |
|
| variant_recalibration_snps_indels_recalibration | File |
The output recalibration file used by ApplyVQSR in INDEL mode |
https://w3id.org/cwl/view/git/f07a07037e7c162f117b3706614d885741a44518/subworkflows/exomeseq-gatk4-02-variantdiscovery.cwl
