diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index e8d6bc76c..136285d3f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -211,8 +211,10 @@ public class VariantFiltrationWalker extends RodWalker { filters.add(CLUSTERED_SNP_FILTER_NAME); for ( VariantContextUtils.JexlVCMatchExp exp : filterExps ) { - if ( VariantContextUtils.match(vc, exp) ) - filters.add(exp.name); + try { + if ( VariantContextUtils.match(vc, exp) ) + filters.add(exp.name); + } catch (Exception e) {} // do nothing; it just means that the expression isn't defined for this context } VariantContext filteredVC;