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 982aef9cb..97ff0b63b 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -119,7 +119,8 @@ public class VariantFiltrationWalker extends RodWalker { addFilter(filterString, "SnpCluster"); if ( filterExpression != null ) { - Map infoMap = context.second.mCurrentRecord.getInfoValues(); + Map infoMap = new HashMap(context.second.mCurrentRecord.getInfoValues()); + infoMap.put("QUAL", String.valueOf(context.second.mCurrentRecord.getQual())); JexlContext jContext = JexlHelper.createContext(); jContext.setVars(infoMap);