diff --git a/HISTORY.md b/HISTORY.md
index 1e65ab5a6..8e29980fe 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -1,3 +1,5 @@
+## 1.0.9 (in progress)
+
 ## 1.0.8 (5 February 2018)
 
 - GATK4 is the new default GATK release used in bcbio when running HaplotypeCaller or
diff --git a/bcbio/pipeline/cleanbam.py b/bcbio/pipeline/cleanbam.py
index b9572af81..5c443f600 100644
--- a/bcbio/pipeline/cleanbam.py
+++ b/bcbio/pipeline/cleanbam.py
@@ -55,7 +55,10 @@ def remove_extracontigs(in_bam, data):
             rg_info = novoalign.get_rg_info(data["rgnames"])
             bcbio_py = sys.executable
             ref_file = dd.get_ref_file(data)
-            cmd = ("samtools view -h {in_bam} {str_chroms} | "
+            local_bam = os.path.join(os.path.dirname(tx_out_file), os.path.basename(in_bam))
+            utils.symlink_plus(in_bam, local_bam)
+            bam.index(local_bam, data["config"])
+            cmd = ("samtools view -h {local_bam} {str_chroms} | "
                    """{bcbio_py} -c 'from bcbio.pipeline import cleanbam; """
                    """cleanbam.fix_header("{ref_file}")' | """
                    "samtools view -u - | "
diff --git a/setup.py b/setup.py
index 69571348b..494a71424 100755
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,7 @@
 import os
 from setuptools import setup, find_packages
 
-version = "1.0.8"
+version = "1.0.9a0"
 
 def write_version_py():
     version_py = os.path.join(os.path.dirname(__file__), 'bcbio', 'pipeline',