diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala
index 8f19a1f..3322804 100644
--- a/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala
+++ b/cli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala
@@ -83,7 +83,7 @@ class Freebayes(protected val args: FreebayesArgs) extends BDGSparkCommand[Freeb
     val input: AlignmentRecordRDD = sc.loadAlignments(args.inputPath, stringency = stringency)
 
     implicit val tFormatter = BAMInFormatter
-    implicit val uFormatter = new VCFOutFormatter
+    implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration)
 
     val freebayesCommand = if (args.useDocker) {
       Seq("docker",
diff --git a/cli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala b/cli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala
index 45356dd..bdf8fb0 100644
--- a/cli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala
+++ b/cli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala
@@ -86,7 +86,7 @@ class SnpEff(protected val args: SnpEffArgs) extends BDGSparkCommand[SnpEffArgs]
     val input: VariantContextRDD = sc.loadVcf(args.inputPath, stringency)
 
     implicit val tFormatter = VCFInFormatter
-    implicit val uFormatter = new VCFOutFormatter
+    implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration)
 
     val snpEffCommand = if (args.useDocker) {
       Seq("docker",