diff --git a/src/subcommand/gbwt_main.cpp b/src/subcommand/gbwt_main.cpp
index 4eca4e47a8..e7d2609187 100644
--- a/src/subcommand/gbwt_main.cpp
+++ b/src/subcommand/gbwt_main.cpp
@@ -158,7 +158,7 @@ void validate_gbwt_config(GBWTConfig& config);
 
 void step_1_build_gbwts(GBWTHandler& gbwts, GraphHandler& graphs, GBWTConfig& config);
 void step_2_merge_gbwts(GBWTHandler& gbwts, GBWTConfig& config);
-void step_3_alter_gbwt(GBWTHandler& gbwts, GBWTConfig& config);
+void step_3_alter_gbwt(GBWTHandler& gbwts, GraphHandler& graphs, GBWTConfig& config);
 void step_4_path_cover(GBWTHandler& gbwts, GraphHandler& graphs, GBWTConfig& config);
 void step_5_gbwtgraph(GBWTHandler& gbwts, GraphHandler& graphs, GBWTConfig& config);
 void step_6_r_index(GBWTHandler& gbwts, GBWTConfig& config);
@@ -195,7 +195,7 @@ int main_gbwt(int argc, char** argv) {
 
     // Edit the GBWT (remove samples, apply tags).
     if (!config.to_remove.empty() || !config.tags_to_set.empty()) {
-        step_3_alter_gbwt(gbwts, config);
+        step_3_alter_gbwt(gbwts, graphs, config);
     }
 
     // Path cover construction.
@@ -1501,28 +1501,38 @@ void remove_samples(GBWTHandler& gbwts, GBWTConfig& config) {
     report_time_memory("Samples removed", start, config);
 }
 
-void set_tags(GBWTHandler& gbwts, GBWTConfig& config) {
+void set_tags(GBWTHandler& gbwts, GraphHandler& graphs, GBWTConfig& config) {
     double start = gbwt::readTimer();
     if (config.show_progress) {
         std::cerr << "Setting " << config.tags_to_set.size() << " tags on the GBWT" << std::endl;
     }
     
     gbwts.use_compressed();
+    bool set_reference_samples = false;
     for (auto& kv : config.tags_to_set) {
-        gbwts.compressed.tags.set(kv.first, kv.second); 
+        gbwts.compressed.tags.set(kv.first, kv.second);
+        if (kv.first == gbwtgraph::REFERENCE_SAMPLE_LIST_GBWT_TAG) {
+            set_reference_samples = true;
+        }
     }
     // We modified the GBWT (we assume some tags got set)
     gbwts.unbacked();
-    
+
+    // If we updated reference samples and have an existing GBWTGraph, we need to recache the named paths.
+    // This is because we may want to include the reference paths in a path cover GBWT.
+    if (set_reference_samples && (graphs.in_use == GraphHandler::graph_gbwtgraph || graphs.in_use == GraphHandler::graph_gbz)) {
+        graphs.gbwt_graph->set_gbwt(gbwts.compressed);
+    }
+
     report_time_memory("Tags set", start, config);
 }
 
-void step_3_alter_gbwt(GBWTHandler& gbwts, GBWTConfig& config) {
+void step_3_alter_gbwt(GBWTHandler& gbwts, GraphHandler& graphs, GBWTConfig& config) {
     if (!config.to_remove.empty()) {
         remove_samples(gbwts, config);
     }
     if (!config.tags_to_set.empty()) {
-        set_tags(gbwts, config);
+        set_tags(gbwts, graphs, config);
     }
 }
 
diff --git a/test/t/37_vg_gbwt.t b/test/t/37_vg_gbwt.t
index a5849bc47a..4260f5f596 100644
--- a/test/t/37_vg_gbwt.t
+++ b/test/t/37_vg_gbwt.t
@@ -5,7 +5,7 @@ BASH_TAP_ROOT=../deps/bash-tap
 
 PATH=../bin:$PATH # for vg
 
-plan tests 155
+plan tests 161
 
 
 # Build vg graphs for two chromosomes
@@ -330,7 +330,16 @@ is $(vg gbwt -H large.local.gbwt) 18 "local haplotypes w/ reference paths: 18 ha
 is $(vg gbwt -S large.local.gbwt) 18 "local haplotypes w/ reference paths: 18 samples"
 is $(vg gbwt --tags large.local.gbwt | grep -c reference_samples) 1 "local haplotypes w/ reference paths: reference_samples set"
 
-rm -f large.gbz large.local.gbwt
+# Now the same but with a specified reference sample
+vg gbwt -Z large.gbz -l -n 16 --pass-paths --set-reference GRCh38 -o large.local.GCRh38.gbwt
+is $? 0 "Local haplotypes with a specified reference sample"
+is $(vg gbwt -c large.local.GCRh38.gbwt) 34 "local haplotypes w/ reference paths: 34 paths"
+is $(vg gbwt -C large.local.GCRh38.gbwt) 2 "local haplotypes w/ reference paths: 2 contigs"
+is $(vg gbwt -H large.local.GCRh38.gbwt) 17 "local haplotypes w/ reference paths: 17 haplotypes"
+is $(vg gbwt -S large.local.GCRh38.gbwt) 17 "local haplotypes w/ reference paths: 17 samples"
+is $(vg gbwt --tags large.local.GCRh38.gbwt | grep -c reference_samples) 1 "local haplotypes w/ reference paths: reference_samples set"
+
+rm -f large.gbz large.local.gbwt large.local.GCRh38.gbwt
 
 
 # Build GBWTGraph from an augmented GBWT