diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
index 1857f605dde..6d17a547d32 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
@@ -4,10 +4,12 @@
 import org.broadinstitute.barclay.argparser.Advanced;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.ArgumentCollection;
+import org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters;
 import org.broadinstitute.hellbender.engine.FeatureInput;
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
 import org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter;
 import org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner;
+import org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignmentConstants;
 
 /**
  * Set of arguments for Assembly Based Callers
@@ -34,6 +36,26 @@ public abstract class AssemblyBasedCallerArgumentCollection {
 
     public static final String PILEUP_DETECTION_LONG_NAME = "pileup-detection";
 
+    public static final String SMITH_WATERMAN_DANGLING_END_MATCH_VALUE_LONG_NAME = "smith-waterman-dangling-end-match-value";
+    public static final String SMITH_WATERMAN_DANGLING_END_MISMATCH_PENALTY_LONG_NAME = "smith-waterman-dangling-end-mismatch-penalty";
+    public static final String SMITH_WATERMAN_DANGLING_END_GAP_OPEN_PENALTY_LONG_NAME = "smith-waterman-dangling-end-gap-open-penalty";
+    public static final String SMITH_WATERMAN_DANGLING_END_GAP_EXTEND_PENALTY_LONG_NAME = "smith-waterman-dangling-end-gap-extend-penalty";
+    public static final String SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MATCH_VALUE_LONG_NAME = "smith-waterman-haplotype-to-reference-match-value";
+    public static final String SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MISMATCH_PENALTY_LONG_NAME = "smith-waterman-haplotype-to-reference-mismatch-penalty";
+    public static final String SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_OPEN_PENALTY_LONG_NAME = "smith-waterman-haplotype-to-reference-gap-open-penalty";
+    public static final String SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_EXTEND_PENALTY_LONG_NAME = "smith-waterman-haplotype-to-reference-gap-extend-penalty";
+    public static final String SMITH_WATERMAN_READ_TO_HAPLOTYPE_MATCH_VALUE_LONG_NAME = "smith-waterman-read-to-haplotype-match-value";
+    public static final String SMITH_WATERMAN_READ_TO_HAPLOTYPE_MISMATCH_PENALTY_LONG_NAME = "smith-waterman-read-to-haplotype-mismatch-penalty";
+    public static final String SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_OPEN_PENALTY_LONG_NAME = "smith-waterman-read-to-haplotype-gap-open-penalty";
+    public static final String SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_EXTEND_PENALTY_LONG_NAME = "smith-waterman-read-to-haplotype-gap-extend-penalty";
+
+    /** See documentation at {@link SmithWatermanAlignmentConstants#STANDARD_NGS}. */
+    private static final SWParameters DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS = SmithWatermanAlignmentConstants.STANDARD_NGS;
+    /** See documentation at {@link SmithWatermanAlignmentConstants#NEW_SW_PARAMETERS}. */
+    private static final SWParameters DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS = SmithWatermanAlignmentConstants.NEW_SW_PARAMETERS;
+    /** See documentation at {@link SmithWatermanAlignmentConstants#ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS}. */
+    private static final SWParameters DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS = SmithWatermanAlignmentConstants.ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS;
+
     public ReadThreadingAssembler createReadThreadingAssembler() {
         final ReadThreadingAssembler assemblyEngine = assemblerArgs.makeReadThreadingAssembler();
         assemblyEngine.setDebug(assemblerArgs.debugAssembly);
@@ -153,4 +175,132 @@ public ReadThreadingAssembler createReadThreadingAssembler() {
                     "that overlap the variant or any base no further than this distance expressed in base pairs",
             optional = true)
     public int informativeReadOverlapMargin = 2;
-}
+
+    /**
+     * Enables pileup-based haplotype creation and variant detection
+     *
+     * NOTE: --pileup-detection is a beta feature. Use this mode at your own risk.
+     */
+    @Argument(fullName= PILEUP_DETECTION_LONG_NAME, doc = "If enabled, the variant caller will create pileup-based haplotypes in addition to the assembly-based haplotype generation.", optional = true)
+    public boolean usePileupDetection = false;
+
+
+    // -----------------------------------------------------------------------------------------------
+    // Smith-Waterman parameters for dangling-end recovery
+    // -----------------------------------------------------------------------------------------------
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_DANGLING_END_MATCH_VALUE_LONG_NAME,
+            doc = "Smith-Waterman match value for dangling-end recovery.",
+            minValue = 0,
+            optional = true)
+    public int smithWatermanDanglingEndMatchValue = DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS.getMatchValue();
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_DANGLING_END_MISMATCH_PENALTY_LONG_NAME,
+            doc = "Smith-Waterman mismatch penalty for dangling-end recovery.",
+            maxValue = 0,
+            optional = true)
+    public int smithWatermanDanglingEndMismatchPenalty = DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS.getMismatchPenalty();
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_DANGLING_END_GAP_OPEN_PENALTY_LONG_NAME,
+            doc = "Smith-Waterman gap-open penalty for dangling-end recovery.",
+            maxValue = 0,
+            optional = true)
+    public int smithWatermanDanglingEndGapOpenPenalty = DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS.getGapOpenPenalty();
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_DANGLING_END_GAP_EXTEND_PENALTY_LONG_NAME,
+            doc = "Smith-Waterman gap-extend penalty for dangling-end recovery.",
+            maxValue = 0,
+            optional = true)
+    public int smithWatermanDanglingEndGapExtendPenalty = DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS.getGapExtendPenalty();
+
+    // -----------------------------------------------------------------------------------------------
+    // Smith-Waterman parameters for haplotype-to-reference alignment
+    // -----------------------------------------------------------------------------------------------
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MATCH_VALUE_LONG_NAME,
+            doc = "Smith-Waterman match value for haplotype-to-reference alignment.",
+            minValue = 0,
+            optional = true)
+    public int smithWatermanHaplotypeToReferenceMatchValue = DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS.getMatchValue();
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MISMATCH_PENALTY_LONG_NAME,
+            doc = "Smith-Waterman mismatch penalty for haplotype-to-reference alignment.",
+            maxValue = 0,
+            optional = true)
+    public int smithWatermanHaplotypeToReferenceMismatchPenalty = DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS.getMismatchPenalty();
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_OPEN_PENALTY_LONG_NAME,
+            doc = "Smith-Waterman gap-open penalty for haplotype-to-reference alignment.",
+            maxValue = 0,
+            optional = true)
+    public int smithWatermanHaplotypeToReferenceGapOpenPenalty = DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS.getGapOpenPenalty();
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_EXTEND_PENALTY_LONG_NAME,
+            doc = "Smith-Waterman gap-extend penalty for haplotype-to-reference alignment.",
+            maxValue = 0,
+            optional = true)
+    public int smithWatermanHaplotypeToReferenceGapExtendPenalty = DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS.getGapExtendPenalty();
+
+    // -----------------------------------------------------------------------------------------------
+    // Smith-Waterman parameters for read-to-haplotype alignment
+    // -----------------------------------------------------------------------------------------------
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_READ_TO_HAPLOTYPE_MATCH_VALUE_LONG_NAME,
+            doc = "Smith-Waterman match value for read-to-haplotype alignment.",
+            minValue = 0,
+            optional = true)
+    public int smithWatermanReadToHaplotypeMatchValue = DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS.getMatchValue();
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_READ_TO_HAPLOTYPE_MISMATCH_PENALTY_LONG_NAME,
+            doc = "Smith-Waterman mismatch penalty for read-to-haplotype alignment.",
+            maxValue = 0,
+            optional = true)
+    public int smithWatermanReadToHaplotypeMismatchPenalty = DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS.getMismatchPenalty();
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_OPEN_PENALTY_LONG_NAME,
+            doc = "Smith-Waterman gap-open penalty for read-to-haplotype alignment.",
+            maxValue = 0,
+            optional = true)
+    public int smithWatermanReadToHaplotypeGapOpenPenalty = DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS.getGapOpenPenalty();
+
+    @Advanced
+    @Argument(fullName = SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_EXTEND_PENALTY_LONG_NAME,
+            doc = "Smith-Waterman gap-extend penalty for read-to-haplotype alignment.",
+            maxValue = 0,
+            optional = true)
+    public int smithWatermanReadToHaplotypeGapExtendPenalty = DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS.getGapExtendPenalty();
+
+    public SWParameters getDanglingEndSWParameters() {
+        return new SWParameters(
+                smithWatermanDanglingEndMatchValue,
+                smithWatermanDanglingEndMismatchPenalty,
+                smithWatermanDanglingEndGapOpenPenalty,
+                smithWatermanDanglingEndGapExtendPenalty);
+    }
+
+    public SWParameters getHaplotypeToReferenceSWParameters() {
+        return new SWParameters(
+                smithWatermanHaplotypeToReferenceMatchValue,
+                smithWatermanHaplotypeToReferenceMismatchPenalty,
+                smithWatermanHaplotypeToReferenceGapOpenPenalty,
+                smithWatermanHaplotypeToReferenceGapExtendPenalty);
+    }
+
+    public SWParameters getReadToHaplotypeSWParameters() {
+        return new SWParameters(
+                smithWatermanReadToHaplotypeMatchValue,
+                smithWatermanReadToHaplotypeMismatchPenalty,
+                smithWatermanReadToHaplotypeGapOpenPenalty,
+                smithWatermanReadToHaplotypeGapExtendPenalty);
+    }
\ No newline at end of file