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JEXL Select of ANN in INFO field

petersampetersam PortlandMember

I have a vcf file that includes annotations added with SNPeff. I would like to use SelectVariants to pull variant sites based on that annotation.The field is characterized as

INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">

I have used SelectVariants with JEXL commands to generate lists based on other attributes like sample genotype or AC. I would like to generate a list of all variants that are classified as "HIGH" in the Annotation_Impact field. Could somebody suggest the proper JEXL format to do this?

Thank uou

Best Answer


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