diff --git a/deps/libbdsg b/deps/libbdsg
index 1c1df7b1b5..c075778651 160000
--- a/deps/libbdsg
+++ b/deps/libbdsg
@@ -1 +1 @@
-Subproject commit 1c1df7b1b541894f6413ed4a2cbefbd0565955af
+Subproject commit c075778651956b27f212360bca8cff502b2abfc4
diff --git a/src/subcommand/call_main.cpp b/src/subcommand/call_main.cpp
index 25cc1d6ea2..af8ee3cb89 100644
--- a/src/subcommand/call_main.cpp
+++ b/src/subcommand/call_main.cpp
@@ -435,6 +435,8 @@ int main_call(int argc, char** argv) {
     // Apply overlays as necessary
     bool need_path_positions = vcf_filename.empty();
     bool need_vectorizable = !pack_filename.empty();
+    // When not using GBWT/GBZ, embedded HAPLOTYPE paths are the sample alleles
+    bool all_paths = gbwt_filename.empty() && !gbz_graph;
     bdsg::ReferencePathOverlayHelper pp_overlay_helper;
     bdsg::ReferencePathVectorizableOverlayHelper ppv_overlay_helper;
     bdsg::PathVectorizableOverlayHelper pv_overlay_helper;
@@ -444,7 +446,7 @@ int main_call(int argc, char** argv) {
     if (need_path_positions && need_vectorizable) {
         graph = dynamic_cast<PathHandleGraph*>(ppv_overlay_helper.apply(graph));
     } else if (need_path_positions && !need_vectorizable) {
-        graph = dynamic_cast<PathHandleGraph*>(pp_overlay_helper.apply(graph));
+        graph = dynamic_cast<PathHandleGraph*>(pp_overlay_helper.apply(graph, all_paths));
     } else if (!need_path_positions && need_vectorizable) {
         graph = dynamic_cast<PathHandleGraph*>(pv_overlay_helper.apply(graph));
     }
diff --git a/src/subcommand/deconstruct_main.cpp b/src/subcommand/deconstruct_main.cpp
index aa98720aaf..405fbfc70b 100644
--- a/src/subcommand/deconstruct_main.cpp
+++ b/src/subcommand/deconstruct_main.cpp
@@ -258,7 +258,9 @@ int main_deconstruct(int argc, char** argv) {
     std::chrono::time_point<std::chrono::system_clock> overlay_start_time = std::chrono::system_clock::now(); 
     
     // Make the overlay
-    PathPositionHandleGraph* graph = overlay_helper.apply(path_handle_graph);
+    // When not using GBWT/GBZ, embedded HAPLOTYPE paths are the sample alleles
+    bool all_paths = gbwt_file_name.empty() && !gbz_graph;
+    PathPositionHandleGraph* graph = overlay_helper.apply(path_handle_graph, all_paths);
     
     // See how long that took
     clock_t overlay_stop_clock = clock();