diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index f15543bd4de..10a053d28eb 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -12,6 +12,7 @@ import sys
 import tarfile
 import tempfile
 import zipfile
+from collections import OrderedDict
 from json import dumps
 
 import h5py
@@ -234,10 +235,10 @@ class BamNative(Binary):
             # TODO: Reference names, lengths, read_groups and headers can become very large, truncate when necessary
             dataset.metadata.reference_names = list(bam_file.references)
             dataset.metadata.reference_lengths = list(bam_file.lengths)
-            dataset.metadata.bam_header = bam_file.header
+            dataset.metadata.bam_header = OrderedDict((k, v) for k, v in bam_file.header.items())
             dataset.metadata.read_groups = [read_group['ID'] for read_group in dataset.metadata.bam_header.get('RG', []) if 'ID' in read_group]
-            dataset.metadata.sort_order = bam_file.header.get('HD', {}).get('SO', None)
-            dataset.metadata.bam_version = bam_file.header.get('HD', {}).get('VN', None)
+            dataset.metadata.sort_order = dataset.metadata.bam_header.get('HD', {}).get('SO', None)
+            dataset.metadata.bam_version = dataset.metadata.bam_header.get('HD', {}).get('VN', None)
         except Exception:
             # Per Dan, don't log here because doing so will cause datasets that
             # fail metadata to end in the error state
@@ -383,25 +384,12 @@ class Bam(BamNative):
 
     def set_meta(self, dataset, overwrite=True, **kwd):
         # These metadata values are not accessible by users, always overwrite
+        super(Bam, self).set_meta(dataset=dataset, overwrite=overwrite, **kwd)
         index_file = dataset.metadata.bam_index
         if not index_file:
             index_file = dataset.metadata.spec['bam_index'].param.new_file(dataset=dataset)
         pysam.index(dataset.file_name, index_file.file_name)
         dataset.metadata.bam_index = index_file
-        # Now use pysam with BAI index to determine additional metadata
-        try:
-            bam_file = pysam.AlignmentFile(dataset.file_name, mode='rb', index_filename=index_file.file_name)
-            # TODO: Reference names, lengths, read_groups and headers can become very large, truncate when necessary
-            dataset.metadata.reference_names = list(bam_file.references)
-            dataset.metadata.reference_lengths = list(bam_file.lengths)
-            dataset.metadata.bam_header = bam_file.header
-            dataset.metadata.read_groups = [read_group['ID'] for read_group in dataset.metadata.bam_header.get('RG', []) if 'ID' in read_group]
-            dataset.metadata.sort_order = bam_file.header.get('HD', {}).get('SO', None)
-            dataset.metadata.bam_version = bam_file.header.get('HD', {}).get('VN', None)
-        except Exception:
-            # Per Dan, don't log here because doing so will cause datasets that
-            # fail metadata to end in the error state
-            pass
 
     def sniff(self, file_name):
         return super(Bam, self).sniff(file_name) and not self.dataset_content_needs_grooming(file_name)
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index adddb8247b9..dd1ccc5f58a 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -11,7 +11,7 @@ mercurial==3.7.3; python_version < '3.0'
 pycrypto==2.6.1
 uWSGI==2.0.15
 # Flexible BAM index naming is new to core pysam
-pysam>=0.13
+pysam==0.14
 
 # Install python_lzo if you want to support indexed access to lzo-compressed
 # locally cached maf files via bx-python