diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index 6f98e0547..d5b291808 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -124,6 +124,8 @@ class fullCallingPipeline extends QScript {
         realigner.intervals = Nil
         realigner.intervalsString = Nil
         realigner.scatterCount = num_cleaner_scatter_jobs min contigs.size
+        realigner.DBSNP = qscript.pipeline.getProject.getDbsnpFile
+        realigner.rodbind :+= RodBind("indels", "VCF", swapExt(qscript.pipeline.getProject.getReferenceFile, "fasta", "1kg_pilot_indels.vcf") 
 
         // if scatter count is > 1, do standard scatter gather, if not, explicitly set up fix mates
         if (realigner.scatterCount > 1) {