diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java index 8092f8c1a..3bb6ee3f2 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java @@ -250,9 +250,13 @@ public class RecalDataManager { ((GATKSAMRecord)read).setReadGroup( readGroup ); } - if( RAC.FORCE_PLATFORM != null && !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM)) { + if( RAC.FORCE_PLATFORM != null && (readGroup.getPlatform() == null || !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM))) { readGroup.setPlatform( RAC.FORCE_PLATFORM ); } + + if ( readGroup.getPlatform() == null ) { + readGroup.setPlatform( RAC.DEFAULT_PLATFORM ); + } } /**