Variant Annotation with VEP (Variant Effect Predictor) from GATK .gvcf files

Created: 2016-05-16 19:16:39 Last updated: 2016-07-06 15:33:48

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Here, from a list of g.vcf files, we execute GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller

Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html

The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
g_VCFs	Comma separated list of g.vcf files
Ouput_path	The path in which files will be written. If it does not exists, the folder will be created.
Project_Name	Project name. This will be the name you final vcf will recieve.

Processors (7)

Name	Type	Description
VEP	stringconstant	Complete path to the VEP perl file. http://www.ensembl.org/info/docs/tools/vep/script/index.html Value /home/murilo/Dropbox/Doutorado/Taverna/tavernaTeste/ensembl-tools-release-84/scripts/variant_effect_predictor/variant_effect_predictor.pl
GATK	stringconstant	Complete path to GATK jar file. https://www.broadinstitute.org/gatk/download/ Value /home/murilo/Dropbox/Doutorado/Taverna/tavernaTeste/picard-tools-1.141/GenomeAnalysisTK.jar
GATK_GenotypeGVCFs	externaltool	Here we generate a list of g.vcfs to enter the GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller
REF	stringconstant	Reference genome. Notice you must index the fasta file as in http://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference and with "bwa index" command. Value /home/murilo/Dropbox/Doutorado/Taverna/tavernaTeste/REF/genome.fa
DBSNP	stringconstant	Location to a VCF file containing variations from DBSNP. ftp://ftp.ncbi.nih.gov/snp/ Value /home/murilo/Dropbox/Doutorado/Taverna/tavernaTeste/dbsnp.vcf
VEP_Variant_Effect_Predictor	externaltool	Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Save_VCF	externaltool	Saves the resulting vcf file from the workflow

Beanshells (0)

Outputs (2)

Name	Description
STDERR
FINAL_VCF

Datalinks (12)

Source	Sink
GATK:value	GATK_GenotypeGVCFs:GATK
REF:value	GATK_GenotypeGVCFs:REF
DBSNP:value	GATK_GenotypeGVCFs:DBSNP
g_VCFs	GATK_GenotypeGVCFs:g_VCFs
GATK_GenotypeGVCFs:VCF	VEP_Variant_Effect_Predictor:VCF
VEP:value	VEP_Variant_Effect_Predictor:VEP
VEP_Variant_Effect_Predictor:VEP_VCF	Save_VCF:FILENAME
Ouput_path	Save_VCF:PATH_OUT
Project_Name	Save_VCF:PROJECT_NAME
GATK_GenotypeGVCFs:STDERR	STDERR
VEP_Variant_Effect_Predictor:STDERR	STDERR
VEP_Variant_Effect_Predictor:VEP_VCF	FINAL_VCF