diff --git a/haptools/data/genotypes.py b/haptools/data/genotypes.py
index 953d8210..dce237a3 100644
--- a/haptools/data/genotypes.py
+++ b/haptools/data/genotypes.py
@@ -805,7 +805,13 @@ def write(self):
                     record.samples[sample].phased = self.data[samp_idx, var_idx, 2]
             # write the record to a file
             vcf.write(record)
-        vcf.close()
+        try:
+            vcf.close()
+        except OSError as e:
+            if e.errno == 9 and len(self.variants) == 0:
+                self.log.warning("No variants to write to VCF")
+            else:
+                raise e
 
 
 class TRRecordHarmonizerRegion(trh.TRRecordHarmonizer):
diff --git a/haptools/data/haplotypes.py b/haptools/data/haplotypes.py
index ba33d0a5..1723be0e 100644
--- a/haptools/data/haplotypes.py
+++ b/haptools/data/haplotypes.py
@@ -1198,9 +1198,13 @@ def __iter__(
         indexed = True
         try:
             haps_file = TabixFile(str(self.fname))
+            if region is not None:
+                haps_file.fetch(region=region, multiple_iterators=True)
         except OSError:
             indexed = False
-        # if the user requested a specific region or subset of haplotypes and the file
+        except ValueError:
+            indexed = False
+        # If the user requested a specific region or subset of haplotypes and the file
         # is indexed, then we should handle it using tabix
         # else, we use a regular text opener - b/c there's no benefit to using tabix
         if (region or haplotypes) and indexed: