diff --git a/R/inferCNV.R b/R/inferCNV.R
index 026564a2..2972cf3f 100755
--- a/R/inferCNV.R
+++ b/R/inferCNV.R
@@ -233,7 +233,8 @@ create_sep_list <- function(row_count,
 #             row, not the first row.
 split_references <- function(average_data,
                              ref_obs,
-                             num_groups){
+                             num_groups,
+                             hclust_method='complete') {
     logging::loginfo(paste("::split_references:Start", sep=""))
     ret_groups <- list()
     split_groups <- NULL
@@ -269,7 +270,8 @@ split_references <- function(average_data,
         # Get HCLUST
         # Get reference observations only.
         average_reference_obs <- t(average_data[, ref_obs, drop=FALSE])
-        hc <- hclust(dist(average_reference_obs))
+        
+        hc <- hclust(dist(average_reference_obs), method=hclust_method)
 
         split_groups <- cutree(hc, k=num_groups)
         split_groups <- split_groups[hc$order]
@@ -456,14 +458,16 @@ infer_cnv <- function(data,
                       method_bound_vis=NA,
                       lower_bound_vis=NA,
                       upper_bound_vis=NA,
-                      ref_subtract_method="by_mean") {
+                      ref_subtract_method="by_mean",
+                      hclust_method='complete') {
 
     logging::loginfo(paste("::infer_cnv:Start", sep=""))
     
     # Split the reference data into groups if requested
     groups_ref <- split_references(average_data=data, #data_smoothed,
-                                             ref_obs=reference_obs,
-                                             num_groups=num_ref_groups)
+                                   ref_obs=reference_obs,
+                                   num_groups=num_ref_groups,
+                                   hclust_method=hclust_method)
     logging::loginfo(paste("::infer_cnv:split_reference. ",
                            "found ",length(groups_ref)," reference groups.",
                            sep=""))
@@ -896,6 +900,7 @@ plot_cnv <- function(plot_data,
                      contig_cex=1,
                      k_obs_groups=1,
                      x.center=0,
+                     hclust_method='average',
                      color_safe_pal=TRUE,
                      pdf_filename="infercnv.pdf"){
 
@@ -994,6 +999,7 @@ plot_cnv <- function(plot_data,
                           contig_lab_size=contig_cex,
                           breaksList=breaksList_t,
                           x.center=x.center,
+                          hclust_method=hclust_method,
                           layout_lmat=force_layout[["lmat"]],
                           layout_lhei=force_layout[["lhei"]],
                           layout_lwid=force_layout[["lwid"]])
@@ -1049,6 +1055,7 @@ plot_cnv_observations <- function(obs_data,
                                   cluster_contig=NULL,
                                   breaksList,
                                   x.center,
+                                  hclust_method="average",
                                   testing=FALSE,
                                   layout_lmat=NULL,
                                   layout_lhei=NULL,
@@ -1085,8 +1092,9 @@ plot_cnv_observations <- function(obs_data,
                                      sep=" ")) 
         }
     }
-    # HCL with a inversely weighted euclidean distance.
-    obs_hcl <- hclust(dist(obs_data[,hcl_group_indices]),"average")
+                                        # HCL with a inversely weighted euclidean distance.
+    logging::loginfo(paste("clustering observations via method: ", hclust_method, sep=""))
+    obs_hcl <- hclust(dist(obs_data[,hcl_group_indices]), method=hclust_method)
     obs_dendrogram <- as.dendrogram(obs_hcl)
     write.tree(as.phylo(obs_hcl),
                file=paste(file_base_name, "observations_dendrogram.txt", sep=.Platform$file.sep))
diff --git a/scripts/inferCNV.R b/scripts/inferCNV.R
index 7cf4d31e..1f0279f7 100755
--- a/scripts/inferCNV.R
+++ b/scripts/inferCNV.R
@@ -14,6 +14,7 @@ C_LEVEL_CHOICES <- names(loglevels)
 # Visualization outlier thresholding and bounding method choices
 C_VIS_OUTLIER_CHOICES <- c("average_bound")
 C_REF_SUBTRACT_METHODS <- c("by_mean", "by_quantiles")
+C_HCLUST_METHODS <- c("ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid")
 
 CHR = "chr"
 START = "start"
@@ -71,7 +72,14 @@ check_arguments <- function(arguments){
                                 paste(C_REF_SUBTRACT_METHODS, collapse=","), sep="") )
         stop("error, must specify acceptable --ref_subtract_method")
     }
-    
+
+
+    if (! (arguments$hclust_method %in% C_HCLUST_METHODS) ) {
+        logging::logerror(paste(":: --hclust_method: acceptable values are: ",
+                                paste(C_HCLUST_METHODS, collapse=","), sep="") )
+        stop("error, must specify acceptable --hclust_method")
+    }
+        
     # Warn that an average of the samples is used in the absence of
     # normal / reference samples
     if (is.null(arguments$reference_observations)){
@@ -292,10 +300,21 @@ pargs <- optparse::add_option(pargs, c("--ref_subtract_method"),
                               action="store",
                               dest="ref_subtract_method",
                               metavar="Reference_Subtraction_Method",
-                              help=paste("Method used to subtract the reference values from the observations. Valid choices are",
+                              help=paste("Method used to subtract the reference values from the observations. Valid choices are: ",
                                          paste(C_REF_SUBTRACT_METHODS, collapse=", "),
                                          " [Default %default]"))
 
+pargs <- optparse::add_option(pargs, c("--hclust_method"),
+                              type="character",
+                              default="complete",
+                              action="store",
+                              dest="hclust_method",
+                              metavar="Hierarchical_Clustering_Method",
+                              help=paste("Method used for hierarchical clustering of cells. Valid choices are: ",
+                                         paste(C_HCLUST_METHODS, collapse=", "),
+                                         " [Default %default]"))
+
+
 
 pargs <- optparse::add_option(pargs,c("--obs_cluster_contig"),
                               type="character",
@@ -542,7 +561,8 @@ ret_list = infercnv::infer_cnv(data=expression_data,
                                method_bound_vis=args$bound_method_vis,
                                lower_bound_vis=bounds_viz[1],
                                upper_bound_vis=bounds_viz[2],
-                               ref_subtract_method=args$ref_subtract_method)
+                               ref_subtract_method=args$ref_subtract_method,
+                               hclust_method=args$hclust_method)
 
 # Log output
 logging::loginfo(paste("::infer_cnv:Writing final data to ",
@@ -582,6 +602,7 @@ if (args$plot_steps) {
                        ref_groups=ret_list[["REF_GROUPS"]],
                        out_dir=args$output_dir,
                        color_safe_pal=args$use_color_safe,
+                       hclust_method=args$hclust_method,
                        title=args$fig_main,
                        obs_title=args$obs_main,
                        ref_title=args$ref_main)