diff --git a/build.sbt b/build.sbt
index c802a5878..cfae5e653 100644
--- a/build.sbt
+++ b/build.sbt
@@ -128,7 +128,7 @@ lazy val root = Project(id="fgbio", base=file("."))
       "org.scala-lang.modules"    %% "scala-xml"      % "2.1.0",
       "com.fulcrumgenomics"       %% "commons"        % "1.4.0",
       "com.fulcrumgenomics"       %% "sopt"           % "1.1.0",
-      "com.github.samtools"       %  "htsjdk"         % "2.24.1-26-ga38c78d-SNAPSHOT" excludeAll(htsjdkExcludes: _*),
+      "com.github.samtools"       %  "htsjdk"         % "3.0.3" excludeAll(htsjdkExcludes: _*),
       "org.apache.commons"        %  "commons-math3"  % "3.6.1",
       "com.beachape"              %% "enumeratum"     % "1.7.0",
       "com.intel.gkl"             %  "gkl"            % "0.8.8",
diff --git a/src/main/scala/com/fulcrumgenomics/vcf/JointVariantContextIterator.scala b/src/main/scala/com/fulcrumgenomics/vcf/JointVariantContextIterator.scala
index 90e0518bc..b38bc23a1 100644
--- a/src/main/scala/com/fulcrumgenomics/vcf/JointVariantContextIterator.scala
+++ b/src/main/scala/com/fulcrumgenomics/vcf/JointVariantContextIterator.scala
@@ -24,6 +24,7 @@
 
 package com.fulcrumgenomics.vcf
 
+import com.fulcrumgenomics.coord.LocatableOrdering
 import com.fulcrumgenomics.fasta.SequenceDictionary
 import htsjdk.variant.variantcontext.{VariantContext, VariantContextComparator}
 
@@ -31,19 +32,14 @@ object JointVariantContextIterator {
   def apply(iters: Seq[Iterator[VariantContext]],
             dict: SequenceDictionary
            ): JointVariantContextIterator = {
-    new JointVariantContextIterator(
-      iters=iters,
-      dictOrComp = Left(dict)
-    )
+    new JointVariantContextIterator(iters = iters, dict = dict)
   }
 
+  @deprecated("VariantContextComparator will no longer compare variant contexts on location alone.")
   def apply(iters: Seq[Iterator[VariantContext]],
             comp: VariantContextComparator
            ): JointVariantContextIterator = {
-    new JointVariantContextIterator(
-      iters=iters,
-      dictOrComp = Right(comp)
-    )
+    throw new NotImplementedError("VariantContextComparator class can no longer order variant contexts on location alone.")
   }
 }
 
@@ -51,30 +47,24 @@ object JointVariantContextIterator {
   * Iterates over multiple variant context iterators such that we return a list of contexts for the union of sites
   * across the iterators.  If samples is given, we subset each variant context to just that sample.
   */
-class JointVariantContextIterator private(iters: Seq[Iterator[VariantContext]],
-                                          dictOrComp: Either[SequenceDictionary, VariantContextComparator]
-                                         )
+class JointVariantContextIterator private(iters: Seq[Iterator[VariantContext]], dict: SequenceDictionary)
 extends Iterator[Seq[Option[VariantContext]]] {
-  import com.fulcrumgenomics.fasta.Converters.ToSAMSequenceDictionary
 
   if (iters.isEmpty) throw new IllegalArgumentException("No iterators given")
 
   private val iterators = iters.map(_.buffered)
-  private val comparator = dictOrComp match {
-    case Left(dict)  => new VariantContextComparator(dict.asSam)
-    case Right(comp) => comp
-  }
+  private val ordering = LocatableOrdering(dict)
 
   def hasNext: Boolean = iterators.exists(_.nonEmpty)
 
   def next(): Seq[Option[VariantContext]] = {
     val minCtx = iterators.filter(_.nonEmpty).map(_.head).sortWith {
-      case (left: VariantContext, right: VariantContext) => comparator.compare(left, right) < 0
+      case (left: VariantContext, right: VariantContext) => ordering.compare(left, right) < 0
     }.head
     // TODO: could use a TreeSet to store the iterators, examine the head of each iterator, then pop the iterator with the min,
     // and add that iterator back in.
-    iterators.zipWithIndex.map { case(iter, idx) =>
-      if (iter.isEmpty || this.comparator.compare(minCtx, iter.head) != 0) None
+    iterators.map { iter =>
+      if (iter.isEmpty || ordering.compare(minCtx, iter.head) != 0) None
       else Some(iter.next())
     }
   }