diff --git a/avocado-cli/src/main/scala/org/bdgenomics/avocado/cli/Reassemble.scala b/avocado-cli/src/main/scala/org/bdgenomics/avocado/cli/Reassemble.scala
index 534cd5a1..23eafb2d 100644
--- a/avocado-cli/src/main/scala/org/bdgenomics/avocado/cli/Reassemble.scala
+++ b/avocado-cli/src/main/scala/org/bdgenomics/avocado/cli/Reassemble.scala
@@ -20,8 +20,7 @@ package org.bdgenomics.avocado.cli
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
-import org.bdgenomics.adam.rdd.read.{ AlignedReadRDD, AlignmentRecordRDD, MDTagging }
-import org.bdgenomics.avocado.realigner.Realigner
+import org.bdgenomics.avocado.realigner.{ ConsensusRealigner, Realigner }
 import org.bdgenomics.utils.cli._
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
@@ -58,6 +57,10 @@ class ReassembleArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs {
     name = "-defer_merging",
     usage = "Defers merging single file output")
   var deferMerging: Boolean = false
+  @Args4jOption(required = false,
+    name = "-use_consensus_realigner",
+    usage = "If provided, uses consensus-mode realigner.")
+  var useConsensusRealigner: Boolean = false
 
   // required by ADAMSaveAnyArgs
   var sortFastqOutput: Boolean = false
@@ -79,7 +82,11 @@ class Reassemble(
     val reads = sc.loadAlignments(args.inputPath)
 
     // realign the reads
-    val reassembledReads = Realigner.realign(reads, args.kmerLength)
+    val reassembledReads = if (args.useConsensusRealigner) {
+      ConsensusRealigner.realign(reads, args.kmerLength)
+    } else {
+      Realigner.realign(reads, args.kmerLength)
+    }
 
     // save the reads
     reassembledReads.save(args)
diff --git a/avocado-core/src/main/scala/org/bdgenomics/avocado/realigner/ConsensusRealigner.scala b/avocado-core/src/main/scala/org/bdgenomics/avocado/realigner/ConsensusRealigner.scala
new file mode 100644
index 00000000..0ba9d487
--- /dev/null
+++ b/avocado-core/src/main/scala/org/bdgenomics/avocado/realigner/ConsensusRealigner.scala
@@ -0,0 +1,64 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.avocado.realigner
+
+import org.bdgenomics.adam.algorithms.consensus.ConsensusGenerator
+import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
+import org.bdgenomics.adam.rdd.variant.VariantRDD
+import org.bdgenomics.avocado.genotyping.DiscoverVariants
+import org.bdgenomics.formats.avro.Variant
+
+object ConsensusRealigner {
+
+  /**
+   * Realigns a set of reads against the reference genome.
+   *
+   * @param reads Reads to realign.
+   * @param kmerLength The length k of the k-mers.
+   * @return Returns the realigned reads.
+   */
+  def realign(reads: AlignmentRecordRDD,
+              kmerLength: Int): AlignmentRecordRDD = {
+
+    // use the realigner to make a first pass over the reads
+    val realignedReads = Realigner.realign(reads, kmerLength)
+
+    // from here, we'll discover any potential variants
+    val variants = filterIndels(DiscoverVariants(realignedReads))
+
+    // we'll pass these discovered variants to ADAM's indel realigner
+    reads.realignIndels(ConsensusGenerator.fromKnownIndels(variants))
+  }
+
+  /**
+   * @param v The variant to filter.
+   * @return Returns false if the variant is a SNV/MNV.
+   */
+  private[realigner] def discardSnvs(v: Variant): Boolean = {
+    v.getReferenceAllele.length != v.getAlternateAllele.length
+  }
+
+  /**
+   * @param rdd The RDD of variants to filter.
+   * @return Returns a new RDD of variants where the SNVs & MNVs have been
+   *   removed and only INDEL variants remain.
+   */
+  private[realigner] def filterIndels(rdd: VariantRDD): VariantRDD = {
+    rdd.transform(r => r.filter(discardSnvs))
+  }
+}
diff --git a/avocado-core/src/main/scala/org/bdgenomics/avocado/util/PrefilterReads.scala b/avocado-core/src/main/scala/org/bdgenomics/avocado/util/PrefilterReads.scala
index 017d32ac..e578f135 100644
--- a/avocado-core/src/main/scala/org/bdgenomics/avocado/util/PrefilterReads.scala
+++ b/avocado-core/src/main/scala/org/bdgenomics/avocado/util/PrefilterReads.scala
@@ -18,7 +18,7 @@
 package org.bdgenomics.avocado.util
 
 import org.bdgenomics.adam.models.SequenceDictionary
-import org.bdgenomics.adam.rdd.read.{ AlignedReadRDD, AlignmentRecordRDD }
+import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
 import org.bdgenomics.formats.avro.AlignmentRecord
 
 private[avocado] trait PrefilterReadsArgs extends Serializable {
@@ -85,7 +85,7 @@ private[avocado] object PrefilterReads extends Serializable {
     val readRdd = rdd.rdd.filter(readFn)
 
     // construct a new aligned read rdd
-    AlignedReadRDD(readRdd, sequences, rdd.recordGroups)
+    AlignmentRecordRDD(readRdd, sequences, rdd.recordGroups)
   }
 
   /**
diff --git a/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala b/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala
index 5a6503c6..cd63a9e6 100644
--- a/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala
+++ b/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala
@@ -20,6 +20,7 @@ package org.bdgenomics.avocado.genotyping
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.avocado.AvocadoFunSuite
 import org.bdgenomics.avocado.models.Observation
+import org.bdgenomics.avocado.realigner.ConsensusRealigner
 import org.bdgenomics.avocado.util.{
   HardFilterGenotypes,
   TestHardFilterGenotypesArgs
@@ -437,14 +438,16 @@ class BiallelicGenotyperSuite extends AvocadoFunSuite {
     })
   }
 
-  ignore("call hom alt C->CCCCT insertion at 1/866511") {
+  sparkTest("call hom alt C->CCCCT insertion at 1/866511") {
     val readPath = resourceUrl("NA12878.chr1.866511.sam")
     val reads = sc.loadAlignments(readPath.toString)
       .transform(rdd => {
         rdd.filter(_.getMapq > 0)
       })
 
-    val gts = BiallelicGenotyper.discoverAndCall(reads,
+    val realignedReads = ConsensusRealigner.realign(reads, 20)
+
+    val gts = BiallelicGenotyper.discoverAndCall(realignedReads,
       2,
       optPhredThreshold = Some(30)).transform(rdd => {
         rdd.filter(gt => gt.getAlleles.forall(_ == GenotypeAllele.ALT))
diff --git a/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/DiscoverVariantsSuite.scala b/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/DiscoverVariantsSuite.scala
index e28ebecc..82dbce6c 100644
--- a/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/DiscoverVariantsSuite.scala
+++ b/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/DiscoverVariantsSuite.scala
@@ -22,7 +22,7 @@ import org.bdgenomics.adam.models.{
   SequenceDictionary,
   SequenceRecord
 }
-import org.bdgenomics.adam.rdd.read.AlignedReadRDD
+import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
 import org.bdgenomics.avocado.AvocadoFunSuite
 import org.bdgenomics.formats.avro.{ AlignmentRecord, Variant }
 
@@ -233,7 +233,7 @@ class DiscoverVariantsSuite extends AvocadoFunSuite {
       snpReadMCigar, snpReadEqCigar,
       insertRead,
       deleteRead))
-    val readRdd = AlignedReadRDD(rdd,
+    val readRdd = AlignmentRecordRDD(rdd,
       SequenceDictionary(
         SequenceRecord("1", 50L),
         SequenceRecord("2", 40L),
diff --git a/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/ConsensusRealignerSuite.scala b/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/ConsensusRealignerSuite.scala
new file mode 100644
index 00000000..b986577b
--- /dev/null
+++ b/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/ConsensusRealignerSuite.scala
@@ -0,0 +1,85 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.avocado.realigner
+
+import org.bdgenomics.adam.models.SequenceDictionary
+import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
+import org.bdgenomics.adam.rdd.variant.VariantRDD
+import org.bdgenomics.formats.avro.Variant
+
+class ConsensusRealignerSuite extends SparkRealignerSuite {
+
+  val allowLegacyCigars = true
+
+  def realign(rdd: AlignmentRecordRDD,
+              kmerLength: Int): AlignmentRecordRDD = {
+    ConsensusRealigner.realign(rdd, kmerLength)
+  }
+
+  val snv = Variant.newBuilder
+    .setStart(0L)
+    .setReferenceAllele("A")
+    .setAlternateAllele("G")
+    .build
+  val mnv = Variant.newBuilder
+    .setStart(1L)
+    .setReferenceAllele("AC")
+    .setAlternateAllele("GT")
+    .build
+  val ins = Variant.newBuilder
+    .setStart(2L)
+    .setReferenceAllele("A")
+    .setAlternateAllele("ACC")
+    .build
+  val del = Variant.newBuilder
+    .setStart(3L)
+    .setReferenceAllele("GCT")
+    .setAlternateAllele("G")
+    .build
+
+  test("filter out a snv") {
+    assert(!ConsensusRealigner.discardSnvs(snv))
+  }
+
+  test("filter out a mnv") {
+    assert(!ConsensusRealigner.discardSnvs(mnv))
+  }
+
+  test("keep an insert") {
+    assert(ConsensusRealigner.discardSnvs(ins))
+  }
+
+  test("keep a deletion") {
+    assert(ConsensusRealigner.discardSnvs(del))
+  }
+
+  sparkTest("filter snv/mnv variants out") {
+    val vRdd = VariantRDD(sc.parallelize(Seq(snv, mnv, ins, del)),
+      SequenceDictionary.empty)
+    val filteredVariants = ConsensusRealigner.filterIndels(vRdd)
+      .rdd
+      .collect
+
+    val variantIds = filteredVariants.map(_.getStart)
+      .toSet
+
+    assert(variantIds.size === 2)
+    assert(variantIds(2L))
+    assert(variantIds(3L))
+  }
+}
diff --git a/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/RealignerSuite.scala b/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/RealignerSuite.scala
index 4c53d2fc..289dbf6d 100644
--- a/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/RealignerSuite.scala
+++ b/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/RealignerSuite.scala
@@ -30,6 +30,8 @@ import org.bdgenomics.formats.avro.AlignmentRecord
 
 class RealignerSuite extends SparkRealignerSuite {
 
+  val allowLegacyCigars = false
+
   def realign(rdd: AlignmentRecordRDD,
               kmerLength: Int): AlignmentRecordRDD = {
     Realigner.realign(rdd, kmerLength)
diff --git a/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/SparkRealignerSuite.scala b/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/SparkRealignerSuite.scala
index d035a413..171d91cb 100644
--- a/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/SparkRealignerSuite.scala
+++ b/avocado-core/src/test/scala/org/bdgenomics/avocado/realigner/SparkRealignerSuite.scala
@@ -24,18 +24,20 @@ import org.bdgenomics.adam.models.{
   RecordGroupDictionary
 }
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.{ AlignedReadRDD, AlignmentRecordRDD }
+import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
 import org.bdgenomics.avocado.AvocadoFunSuite
 import org.bdgenomics.formats.avro.AlignmentRecord
 
 trait SparkRealignerSuite extends AvocadoFunSuite {
 
+  val allowLegacyCigars: Boolean
+
   def realign(rdd: AlignmentRecordRDD,
               kmerLength: Int): AlignmentRecordRDD
 
   def makeAndRealignRdd(reads: Seq[AlignmentRecord],
                         kmerLength: Int): Array[AlignmentRecord] = {
-    val gRdd = AlignedReadRDD(sc.parallelize(reads),
+    val gRdd = AlignmentRecordRDD(sc.parallelize(reads),
       SequenceDictionary(SequenceRecord("ctg", 50L)),
       RecordGroupDictionary(Seq(RecordGroup("rg", "rg"))))
 
@@ -47,11 +49,16 @@ trait SparkRealignerSuite extends AvocadoFunSuite {
   }
 
   sparkTest("realign a set of reads around an insert") {
-    // insertion sequence:
+    // true insertion sequence:
+    // ins: AATGAGACTTACATCATTAAAACCGTGTGGACACA
+    // ref: AATGAGACTTACATCATT__AACCGTGTGGACACA
+    //
+    // test alignment:
+    // X:                       |
     // ins: AATGAGACTTACATCATTAAAACCGTGTGGACACA
-    // ref: AATGAGACTTACATCATTAA__CCGTGTGGACACA
+    // ref: AATGAGACTTACATCATTAAC__CGTGTGGACACA
     val sequence = "AATGAGACTTACATCATTAAAACCGTGTGGACACA"
-    val insertStart = 20
+    val insertStart = 21
     val readLength = insertStart + 6 + 2
 
     // generate 7 reads with a 6bp flank
@@ -65,10 +72,13 @@ trait SparkRealignerSuite extends AvocadoFunSuite {
         .setRecordGroupName("rg")
         .setReadMapped(true)
         .setSequence(sequence.drop(rId).take(readLength))
+        .setQual("*" * readLength)
         .setStart(rId.toLong)
-        .setEnd((rId + readLength - 2 + 1).toLong)
+        .setEnd((rId + insertStart + 6).toLong)
         .setCigar("%dM2I%dM".format(basesBeforeInsert, basesAfterInsert))
-        .setMismatchingPositions((readLength - 2).toString)
+        .setMismatchingPositions("%dC%d".format(basesBeforeInsert - 1,
+          basesAfterInsert))
+        .setMapq(50)
         .build()
     })
 
@@ -81,25 +91,34 @@ trait SparkRealignerSuite extends AvocadoFunSuite {
 
       // these values are different from above because original alignments were
       // not left justified
-      val basesBeforeInsert = insertStart - rId - 2
-      val basesAfterInsert = 8 + rId
-
-      assert(r.getCigar === "%d=2I%d=".format(basesBeforeInsert, basesAfterInsert))
+      val basesBeforeInsert = insertStart - rId - 3
+      val basesAfterInsert = 9 + rId
+
+      if (allowLegacyCigars) {
+        assert(r.getCigar === "%dM2I%dM".format(basesBeforeInsert, basesAfterInsert))
+      } else {
+        assert(r.getCigar === "%d=2I%d=".format(basesBeforeInsert, basesAfterInsert))
+      }
       assert(r.getMismatchingPositions === (readLength - 2).toString)
     })
   }
 
   sparkTest("realign a set of reads around a deletion") {
-    // deletion sequence:
-    // del: AGGTCTGAATGAGACTTA__TCATTAACCGTGTGGACACA
+    // true deletion sequence:
+    // del: AGGTCTGAATGAGACTT__ATCATTAACCGTGTGGACACA
+    // ref: AGGTCTGAATGAGACTTACATCATTAACCGTGTGGACACA
+    //
+    // test alignment:
+    // X:                     |
+    // del: AGGTCTGAATGAGACT__TATCATTAACCGTGTGGACACA
     // ref: AGGTCTGAATGAGACTTACATCATTAACCGTGTGGACACA
     val sequence = "AGGTCTGAATGAGACTTATCATTAACCGTGTGGACACA"
-    val deleteStart = 18
-    val readLength = deleteStart + 8
+    val deleteStart = 16
+    val readLength = deleteStart + 7
 
     // generate 10 reads with a 8bp flank
     val reads = (0 until 10).map(rId => {
-      val basesBeforeDelete = deleteStart - rId
+      val basesBeforeDelete = deleteStart - rId - 1
       val basesAfterDelete = 8 + rId
 
       AlignmentRecord.newBuilder()
@@ -108,10 +127,13 @@ trait SparkRealignerSuite extends AvocadoFunSuite {
         .setRecordGroupName("rg")
         .setReadMapped(true)
         .setSequence(sequence.drop(rId).take(readLength))
+        .setQual("*" * readLength)
         .setStart(rId.toLong)
-        .setEnd((rId + readLength + 2 + 1).toLong)
+        .setEnd((rId + readLength + 2).toLong)
         .setCigar("%dM2D%dM".format(basesBeforeDelete, basesAfterDelete))
-        .setMismatchingPositions("%d^CA%d".format(basesBeforeDelete, basesAfterDelete))
+        .setMismatchingPositions("%d^TA0C%d".format(basesBeforeDelete,
+          basesAfterDelete - 1))
+        .setMapq(50)
         .build()
     })
 
@@ -124,23 +146,30 @@ trait SparkRealignerSuite extends AvocadoFunSuite {
 
       // these values are different from above because original alignments were
       // not left justified
-      val basesBeforeDelete = deleteStart - rId - 1
-      val basesAfterDelete = 9 + rId
+      val basesBeforeDelete = deleteStart - rId
+      val basesAfterDelete = 7 + rId
 
-      assert(r.getCigar === "%d=2D%d=".format(basesBeforeDelete, basesAfterDelete))
+      if (allowLegacyCigars) {
+        assert(r.getCigar === "%dM2D%dM".format(basesBeforeDelete, basesAfterDelete))
+      } else {
+        assert(r.getCigar === "%d=2D%d=".format(basesBeforeDelete, basesAfterDelete))
+      }
       assert(r.getMismatchingPositions === "%d^AC%d".format(basesBeforeDelete, basesAfterDelete))
     })
   }
 
   sparkTest("realigning a read with a repeat will return the original read") {
     val read = AlignmentRecord.newBuilder()
+      .setContigName("ctg")
       .setReadName("A_READ")
       .setReadMapped(true)
       .setStart(10L)
       .setEnd(17L)
       .setSequence("TCAAAAAAGG")
+      .setQual("**********")
       .setCigar("3M4I3M")
       .setMismatchingPositions("6")
+      .setMapq(50)
       .build()
 
     // make into a genomic rdd
diff --git a/avocado-core/src/test/scala/org/bdgenomics/avocado/util/PrefilterReadsSuite.scala b/avocado-core/src/test/scala/org/bdgenomics/avocado/util/PrefilterReadsSuite.scala
index 69bb006d..700a6a9b 100644
--- a/avocado-core/src/test/scala/org/bdgenomics/avocado/util/PrefilterReadsSuite.scala
+++ b/avocado-core/src/test/scala/org/bdgenomics/avocado/util/PrefilterReadsSuite.scala
@@ -24,7 +24,7 @@ import org.bdgenomics.adam.models.{
   SequenceRecord
 }
 import org.bdgenomics.adam.rdd.ADAMContext._
-import org.bdgenomics.adam.rdd.read.AlignedReadRDD
+import org.bdgenomics.adam.rdd.read.AlignmentRecordRDD
 import org.bdgenomics.formats.avro.AlignmentRecord
 
 case class TestPrefilterReadsArgs(var isNotGrc: Boolean = false,
@@ -239,7 +239,7 @@ class PrefilterReadsSuite extends AvocadoFunSuite {
 
   def testRdd(args: PrefilterReadsArgs, numReads: Int, numContigs: Int) {
 
-    val readRdd = AlignedReadRDD(sc.parallelize(reads), sequences, RecordGroupDictionary.empty)
+    val readRdd = AlignmentRecordRDD(sc.parallelize(reads), sequences, RecordGroupDictionary.empty)
     val filteredRdd = PrefilterReads(readRdd, args)
 
     assert(filteredRdd.rdd.count === numReads)
diff --git a/pom.xml b/pom.xml
index f7af4f26..ba734ac5 100644
--- a/pom.xml
+++ b/pom.xml
@@ -15,7 +15,7 @@
   <name>avocado: A Variant Caller, Distributed</name>
   
   <properties>
-    <adam.version>0.21.0</adam.version>
+    <adam.version>0.21.1-SNAPSHOT</adam.version>
     <avro.version>1.8.0</avro.version>
     <java.version>1.8</java.version>
     <scala.version>2.10.4</scala.version>