diff --git a/Dockerfile b/Dockerfile
index 1c49d3e27..6e6874abe 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -53,7 +53,7 @@ RUN cd /home/cactus && rm -rf cactus_env && \
 	 . cactus_env/bin/activate && \
 	 python3 -m pip install -U setuptools pip && \
 	 python3 -m pip install -U -r ./toil-requirement.txt && \
-	 python3 -m pip install -U .
+	 python3 -m pip install -U --no-build-isolation .
 	 
 # prep the hal python install which is not part of the setup
 RUN rm -rf /home/cactus/hal_lib && \
diff --git a/src/cactus/refmap/cactus_graphmap_join.py b/src/cactus/refmap/cactus_graphmap_join.py
index 84de4e53e..f0a80872b 100644
--- a/src/cactus/refmap/cactus_graphmap_join.py
+++ b/src/cactus/refmap/cactus_graphmap_join.py
@@ -1476,9 +1476,16 @@ def vcf_cat(job, vcf_tbi_ids, tag, sort=False, fix_ploidies=True):
                                     ['bcftools', 'view', '-S', all_sample_list_path, '-O', 'z']],
                         outfile=updated_vcf_path)
             vcf_paths[i] = updated_vcf_path
+
+    # -a below requires indexes
+    for vcf_path in vcf_paths:
+        try:
+            cactus_call(parameters=['tabix', '-fp', 'vcf', vcf_path])
+        except:
+            cactus_call(parameters=['bcftools', 'index', '-c', vcf_path])
         
     cat_vcf_path = os.path.join(work_dir, '{}vcf.gz'.format(tag))
-    cactus_call(parameters=['bcftools', 'concat', '-O', 'z', '--threads', str(job.cores)] + \
+    cactus_call(parameters=['bcftools', 'concat', '-a', '-O', 'z', '--threads', str(job.cores)] + \
                 [os.path.basename(vcf_path) for vcf_path in vcf_paths],
                 work_dir=work_dir, outfile=cat_vcf_path)