diff --git a/python/splitIntervalsByContig.py b/python/splitIntervalsByContig.py
new file mode 100644
index 000000000..351fa1320
--- /dev/null
+++ b/python/splitIntervalsByContig.py
@@ -0,0 +1,33 @@
+import sys
+input_file = sys.argv[1]
+file_index = 1
+
+headerLines = list()
+intervals = open(input_file)
+prevContig = None
+outFile = None
+
+def parseContig(line):
+    if( line.find("-") > -1 ): ## format is chr:start-stop
+        return line.split(":")[0]
+    else:
+        return line.split("\t")[0]
+
+for line in open(input_file).readlines():
+    if ( line.startswith("@") ):
+        headerLines.append(line)
+    else:
+        thisContig = parseContig(line)
+        if ( thisContig != prevContig ):
+            file_index += 1
+            try:
+                newOutFile = open(sys.argv[file_index],'w')
+                if ( outFile != None):
+                    outFile.close()
+                outFile = newOutFile
+                for headerline in headerLines:
+                    outFile.write(headerline)
+            except IndexError:
+                print("Error: fewer output files than contigs. Writing remainder to final file.")
+            prevContig = thisContig
+        outFile.write(line)