diff --git a/misopy/sam_to_bam.py b/misopy/sam_to_bam.py
index 1ae7e85..d56ff07 100644
--- a/misopy/sam_to_bam.py
+++ b/misopy/sam_to_bam.py
@@ -24,14 +24,14 @@ def sam_to_bam(sam_filename, output_dir,
 
     # Sort
     print "Sorting BAM file..."
-    sorted_filename = "%s.sorted" %(bam_filename.split(".bam")[0])
-    cmd = "samtools sort %s %s" %(bam_filename,
-                                  sorted_filename)
+    sorted_filename = "%s.sorted.bam" %(bam_filename.split(".bam")[0])
+    cmd = "samtools sort -o %s %s" %(sorted_filename,
+                                     bam_filename)
     print "  - Executing: %s" %(cmd)
     os.system(cmd)
 
     # Index
-    final_filename = "%s.bam" %(sorted_filename)
+    final_filename = "%s" %(sorted_filename)
     print "Indexing BAM..."
     cmd = "samtools index %s" %(final_filename)
     print "  - Executing: %s" %(cmd)