diff --git a/src/fstalign.cpp b/src/fstalign.cpp
index 125cb52..cc9226d 100644
--- a/src/fstalign.cpp
+++ b/src/fstalign.cpp
@@ -635,7 +635,7 @@ void write_stitches_to_nlp(vector<Stitching>& stitches, ofstream &output_nlp_fil
 }
 
 void HandleWer(FstLoader& refLoader, FstLoader& hypLoader, SynonymEngine &engine, const string& output_sbs, const string& output_nlp,
-               AlignerOptions alignerOptions, bool add_inserts_nlp, bool use_case) {
+               AlignerOptions alignerOptions, bool add_inserts_nlp, bool use_case, std::vector<string> ref_extra_columns, std::vector<string> hyp_extra_columns) {
   //  int speaker_switch_context_size, int numBests, int pr_threshold, string symbols_filename,
   //  string composition_approach, bool record_case_stats) {
   auto logger = logger::GetOrCreateLogger("fstalign");
@@ -701,8 +701,7 @@ void HandleWer(FstLoader& refLoader, FstLoader& hypLoader, SynonymEngine &engine
   JsonLogUnigramBigramStats(topAlignment);
   if (!output_sbs.empty()) {
     logger->info("output_sbs = {}", output_sbs);
-    std::vector<string> extra_hyp_columns = {"confidence"};
-    WriteSbs(topAlignment, stitches, output_sbs, std::vector<string>(),extra_hyp_columns);
+    WriteSbs(topAlignment, stitches, output_sbs, ref_extra_columns, hyp_extra_columns);
   }
 
   if (!output_nlp.empty() && !nlp_ref_loader) {
diff --git a/src/fstalign.h b/src/fstalign.h
index 5cbe130..f02f807 100644
--- a/src/fstalign.h
+++ b/src/fstalign.h
@@ -48,16 +48,9 @@ struct AlignerOptions {
   int levenstein_maximum_error_streak = 100;
 };
 
-// original
-// void HandleWer(FstLoader *refLoader, FstLoader *hypLoader, SynonymEngine *engine, string output_sbs, string
-// output_nlp,
-//                int speaker_switch_context_size, int numBests, int pr_threshold, string symbols_filename,
-//                string composition_approach, bool record_case_stats);
-// void HandleAlign(NlpFstLoader *refLoader, CtmFstLoader *hypLoader, SynonymEngine *engine, ofstream &output_nlp_file,
-//                  int numBests, string symbols_filename, string composition_approach);
 
 void HandleWer(FstLoader& refLoader, FstLoader& hypLoader, SynonymEngine &engine, const string& output_sbs, const string& output_nlp,
-               AlignerOptions alignerOptions, bool add_inserts_nlp = false, bool use_case = false);
+               AlignerOptions alignerOptions, bool add_inserts_nlp, bool use_case, std::vector<string> ref_extra_columns, std::vector<string> hyp_extra_columns);
 void HandleAlign(NlpFstLoader &refLoader, CtmFstLoader &hypLoader, SynonymEngine &engine, ofstream &output_nlp_file,
                  AlignerOptions alignerOptions);
 
diff --git a/src/main.cpp b/src/main.cpp
index d87ddbc..bf03942 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -40,6 +40,9 @@ int main(int argc, char **argv) {
   bool disable_cutoffs = false;
   bool disable_hyphen_ignore = false;
 
+  std::vector<string> ref_extra_columns = std::vector<string>();
+  std::vector<string> hyp_extra_columns = std::vector<string>();
+
   CLI::App app("Rev FST Align");
   app.set_help_all_flag("--help-all", "Expand all help");
   app.add_flag("--version", version, "Show fstalign version.");
@@ -97,6 +100,10 @@ int main(int argc, char **argv) {
 
     c->add_option("--composition-approach", composition_approach,
                   "Desired composition logic. Choices are 'standard' or 'adapted'");
+    c->add_option("--ref-extra-cols", ref_extra_columns,
+                  "Extra columns from the reference to include in SBS output.");
+    c->add_option("--hyp-extra-cols", hyp_extra_columns,
+                  "Extra columns from the hypothesis to include in SBS output.");
   }
   get_wer->add_option("--wer-sidecar", wer_sidecar_filename,
                 "WER sidecar json file.");
@@ -180,7 +187,7 @@ int main(int argc, char **argv) {
   }
 
   if (command == "wer") {
-    HandleWer(*ref, *hyp, engine, output_sbs, output_nlp, alignerOptions, add_inserts_nlp, use_case);
+    HandleWer(*ref, *hyp, engine, output_sbs, output_nlp, alignerOptions, add_inserts_nlp, use_case, ref_extra_columns, hyp_extra_columns);
   } else if (command == "align") {
     if (output_nlp.empty()) {
       console->error("the output nlp file must be specified");