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Using JEXL to apply hard filters or select variants based on annotation values - Legacy GATK Forum

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JEXL stands for Java EXpression Language. It’s not a part of the GATK as such; it’s a software library that can be used by Java-based programs like the GATK. It can be used for many things, but in the context of the GATK, it has one very specific use: making it possible to operate on subsets of variants from VCF files based on one or more annotations, using a single command. This is typically done with walkers such as VariantFiltration and SelectVariants. ###2. Basic structure of JEXL expressions for use with the GATK In this context, a JEXL expression is a string (in the computing sense, i.e. a series of characters) that tells the GATK which annotations to look at and what selection rules to apply. JEXL expressions contain three basic components: keys and values, connected by operators. For example, in this simple JEXL expression which selects variants whose quality score is greater than 30: The complete expression must be framed by double quotes. Within this, keys are strings (typica

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