diff --git a/python/AlignBams.py b/python/AlignBams.py
new file mode 100644
index 000000000..ae8845e23
--- /dev/null
+++ b/python/AlignBams.py
@@ -0,0 +1,41 @@
+import os,sys
+from farm_commands import cmd
+
+def run_BWA(bam, paired=True):
+    "Takes a paired end BAM file and outputs an aligned '.aligned.bam' file "
+    lane = 0
+    root = os.path.splitext(bam)[0]
+    print root
+    
+    # BAM to BFQ
+    cmd("/seq/software/picard/current/bin/BamToBfq.jar I="+bam+" LANE="+str(lane)+" FLOWCELL_BARCODE="+root+" PAIRED_RUN=True RUN_BARCODE="+root+" ANALYSIS_DIR=.")
+    
+    # BFQ to FQ
+    root1 = root+"."+str(lane)+".0.1"
+    root2 = root+"."+str(lane)+".0.2"
+    bfq1 = root1+".bfq"
+    bfq2 = root2+".bfq"
+    fq1 = root1+".fq"
+    fq2 = root2+".fq"
+
+    cmd("/seq/dirseq/maq-0.7.1/maq bfq2fastq "+bfq1+" "+fq1)
+    cmd("/seq/dirseq/maq-0.7.1/maq bfq2fastq "+bfq2+" "+fq2)
+
+    # Run BWA
+    sai1 = root1+".sai"
+    sai2 = root2+".sai"
+    cmd("/seq/dirseq/bwa/bwa-0.4.9/bwa aln /humgen/gsa-scr1/ebanks/bwaref/Homo_sapiens_assembly18.fasta "+fq1+" >"+sai1)
+    cmd("/seq/dirseq/bwa/bwa-0.4.9/bwa aln /humgen/gsa-scr1/ebanks/bwaref/Homo_sapiens_assembly18.fasta "+fq2+" >"+sai2)
+    
+    # Pairing
+    alignedsam = root+".aligned.sam"
+    cmd("/seq/dirseq/bwa/bwa-0.4.9/bwa sampe /humgen/gsa-scr1/ebanks/bwaref/Homo_sapiens_assembly18.fasta "+sai1+" "+sai2+" "+fq1+" "+fq2+" > "+alignedsam)
+    
+    # SAM to BAM
+    bam_ref_list = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.bam.ref_list"
+    alignedbam = root+".aligned.bam"
+    cmd("/seq/dirseq/samtools/current/samtools import "+bam_ref_list+" "+alignedsam+" "+alignedbam)
+    
+if __name__ == "__main__":
+    bamfiles = sys.argv[1:]
+