CWL Workflow: exomeseq.cwl#exomeseq-02-variantdiscovery.cwl

Workflow: exomeseq.cwl#exomeseq-02-variantdiscovery.cwl

Fetched 2025-11-02 02:45:45 GMT

Verified with cwltool version 3.1.20221201130942

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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
name	String
GATKJar	File
threads	Integer (Optional)
intervals	File[] (Optional)
study_type	https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl#bespin-types.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

Steps

ID	Runs	Label	Doc
joint_genotyping	exomeseq.cwl#GATK-GenotypeGVCFs.cwl (CommandLineTool)		GATK-GenotypeGVCFs.cwl is developed for CWL consortium Perform joint genotyping on gVCF files produced by HaplotypeCaller
apply_recalibration_snps	exomeseq.cwl#GATK-ApplyRecalibration.cwl (CommandLineTool)
generate_joint_filenames	exomeseq.cwl#generate-joint-filenames.cwl (ExpressionTool)	Generates a set of file names for joint steps based on an input name
generate_annotations_snps	exomeseq.cwl#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
apply_recalibration_indels	exomeseq.cwl#GATK-ApplyRecalibration.cwl (CommandLineTool)
variant_recalibration_snps	exomeseq.cwl#GATK-VariantRecalibrator-SNPs.cwl (CommandLineTool)		GATK-VariantsRecalibrator.cwl is developed for CWL consortium Usage: ``` java -Xmx8G \ -jar gatk.jar -T VariantRecalibrator \ -R [reference_fasta] \ -recalFile $tmpDir/out.recal \ -tranchesFile $tmpDir/out.tranches \ -rscriptFile $tmpDir/out.R \ -nt 4 \ -an MQRankSum -an ReadPosRankSum -an DP -an FS -an QD \ -mode SNP \ -resource:hapmap,known=false,training=true,truth=true,prior=15.0 [hapmap_vcf] \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 [dbsnp_vcf] \ -resource:omni,known=false,training=true,truth=true,prior=12.0 [1komni_vcf] \ -resource:1000G,known=false,training=true,truth=false,prior=10.0 [1ksnp_vcf] ```
generate_annotations_indels	exomeseq.cwl#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	exomeseq.cwl#GATK-VariantRecalibrator-Indels.cwl (CommandLineTool)		GATK-VariantsRecalibrator.cwl is developed for CWL consortium Usage: ``` java -Xmx8G \ -jar gatk.jar -T VariantRecalibrator \ -R [reference_fasta] \ -recalFile $tmpDir/out.recal \ -tranchesFile $tmpDir/out.tranches \ -rscriptFile $tmpDir/out.R \ -nt 4 \ -an MQRankSum -an ReadPosRankSum -an DP -an FS -an QD \ -mode SNP \ -resource:hapmap,known=false,training=true,truth=true,prior=15.0 [hapmap_vcf] \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 [dbsnp_vcf] \ -resource:omni,known=false,training=true,truth=true,prior=12.0 [1komni_vcf] \ -resource:1000G,known=false,training=true,truth=false,prior=10.0 [1ksnp_vcf] ```

Outputs

ID	Type	Doc
joint_raw_variants	File	VCF file from joint genotyping calling
variant_recalibration_snps_vcf	File	The output filtered and recalibrated VCF file in SNP mode in which each variant is annotated with its VQSLOD value
variant_recalibration_snps_recal	File	The output recal file used by ApplyRecalibration in SNP mode
variant_recalibration_snps_rscript	File	The output rscript file generated by the VQSR in SNP mode to aid in visualization of the input data and learned model
variant_recalibration_snps_tranches	File	The output tranches file used by ApplyRecalibration in SNP mode
variant_recalibration_snps_indels_vcf	File	The output filtered and recalibrated VCF file in in which each variant is annotated with its VQSLOD value
variant_recalibration_snps_indels_recal	File	The output recal file used by ApplyRecalibration in INDEL mode
variant_recalibration_snps_indels_rscript	File	The output rscript file generated by the VQSR in INDEL mode to aid in visualization of the input data and learned model
variant_recalibration_snps_indels_tranches	File	The output tranches file used by ApplyRecalibration in INDEL mode

Permalink:

https://w3id.org/cwl/view/git/68c92437c854a200433ee684067f81f13de5d8eb/packed/exomeseq.cwl?part=exomeseq-02-variantdiscovery.cwl