diff --git a/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java index 70b8ed687..28c1a0a4f 100644 --- a/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java +++ b/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java @@ -58,7 +58,11 @@ public class ReadGroupBlackListFilter implements SamRecordFilter { SAMReadGroupRecord samReadGroupRecord = samRecord.getReadGroup(); if (samReadGroupRecord != null) { - Object attribute = samReadGroupRecord.getAttribute(attributeType); + Object attribute; + if ("ID".equals(attributeType) || "RG".equals(attributeType)) + attribute = samReadGroupRecord.getId(); + else + attribute = samReadGroupRecord.getAttribute(attributeType); if (attribute != null && filterEntry.getValue().contains(attribute)) return true; }