diff --git a/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py b/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py
index 16a6700a7..5da9cad62 100755
--- a/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py
+++ b/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py
@@ -2,9 +2,10 @@ import sys
 import os
 import re
 import traceback
+import shlex, subprocess
 from optparse import OptionParser, OptionGroup
 from IndentedHelpFormatterWithNL import *
-
+import time
 
 # Init cmd-line args
 description = """
@@ -24,6 +25,7 @@ parser.add_option("-l", "--locally", dest="run_locally", action="store_true", de
 parser.add_option("-R", "--reference", metavar="PATH", dest="reference", help="Specifies the path of the reference file to use.", default="/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")
 parser.add_option("-n", "--gene-name-columns", dest="gene_name_columns", metavar="GENE_NAMES", help="Comma-separated list of column names that contain gene names. This arg is passed through to the GenomicAnnotator. The GenomicAnnotator docs have more details on this.")
 parser.add_option("-q", "--queue", dest="queue", metavar="QUEUE", help="Specifies the LSF queue to use.", default="solexa")
+parser.add_option("-s", "--num-parallel-processes", dest="num_parallel_processes", metavar="SLOTS", help="How many processes to launch simultaneously. This is only used when the -l option is set.", default="1")
 
 (options, args) = parser.parse_args()
 
@@ -56,6 +58,7 @@ if not os.access(reference, os.R_OK):
     error("Couldn't access reference file: "+ reference)
 
 queue = options.queue
+num_parallel_processes = int(options.num_parallel_processes)
 
 transcript_dir = os.path.dirname(transcript_table)
 logs_dir = os.path.join(transcript_dir,"logs")
@@ -67,11 +70,37 @@ contigs += [ "chr" + str(x) for x in contig_chars ]
 contigs += [ "chr" + str(x) + "_random" for x in set( contig_chars ).difference(set(['M',12,14,20,'X','Y']))  ]    # There are no "_random" chromosomes for chrM,12,14,20,Y
 
 
+
+
 if run:
     print("Deleting any previous logs...")
     os.system("rm " + os.path.join(logs_dir,"bsub_*_log.txt"))
     os.system("mkdir " + logs_dir)
 
+
+running_processes = []
+def execute(command, stdout_filename=None):
+
+    # Wait until a slot becomes open
+    while len( running_processes ) + 1 >= num_parallel_processes:
+        # Check if any have ended
+        for process in running_processes:
+            if process.poll() != None:
+                print("Process [pid=" + str(process.pid) + "] finished with exit status: " + str(process.returncode))
+                running_processes.remove(process)
+                break
+        else:
+            time.sleep(3) # Sleep for 3 seconds before checking again
+
+    # A slot has opened up - start another process
+    stdout = None
+    if stdout_filename:
+        stdout = open(stdout_filename, "w+")
+        
+
+    p = subprocess.Popen(shlex.split(command), stdout=stdout, stderr=subprocess.STDOUT)
+    running_processes.append(p)
+
 for contig in contigs:        
     if contig.count("random") or contig.lower().count("chrm"):
         MEMORY_USAGE = 10  # Gigabytes
@@ -83,18 +112,16 @@ for contig in contigs:
             MEMORY_USAGE = 32
         EXCLUSIVE = ""
             
-    command = "java -Xmx"+str(MEMORY_USAGE)+"g -jar dist/GenomeAnalysisTK.jar -T TranscriptToInfo -l info -R " + reference + " -B transcripts,AnnotatorInputTable,"+transcript_table+" -n "+gene_name_columns+" -o "+ os.path.join(transcript_dir,output_file_prefix) +"-big-table-ucsc-%s.txt -L %s:1+ " % (contig, contig)
-    
-
-    if run_locally:
-        command += " > " + os.path.join(logs_dir,contig+"_log.txt")
-    else:
+    command = "java -Xmx"+str(MEMORY_USAGE)+"g -jar dist/GenomeAnalysisTK.jar -T TranscriptToInfo -l info -nt " + str(num_parallel_processes) + " -R " + reference + " -B transcripts,AnnotatorInputTable,"+transcript_table+" -n "+gene_name_columns+" -o "+ os.path.join(transcript_dir,output_file_prefix) +"-big-table-ucsc-%s.txt -L %s:1+ " % (contig, contig)
+    if not run_locally:
         command = "bsub "+EXCLUSIVE+" -q " + queue + " -R \"rusage[mem="+str(MEMORY_USAGE)+"]\" -o " + os.path.join(logs_dir,contig+"_log.txt") + " "  + command
     
-
-    
     if run:
         print("Executing: " + command)
-        os.system(command)
+        if run_locally:
+            #execute(command, os.path.join(logs_dir,contig+"_log.txt"))
+            execute(command + " >& " + os.path.join(logs_dir,contig+"_log.txt"))
+        else:
+            os.system(command)
     else:
         print(command)