Filtering Variants using the Format Column + JEXL Oddities
Posted in Ask the GATK team | Last updated on


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Hi Team, I have a VCF which I'd like to filter by variant frequency. The problem is, my frequencies are percentages rather than decimals. Is there a workaround in JEXL which allows it to parse the '%' operator as a percentage (or ignore it entirely) rather than considering the field a string upon seeing the modulo operator? The VCF also has two columns in the format column (a normal and a tumor). Is it possible to drill down into these using just the genotypeFilterExpression/genotypeFilterName flags or must do something else?

Thanks, Eric T Dawson


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