diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..e37d154
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "samtools"]
+	path = samtools
+	url = http://github.com/samtools/samtools.git
diff --git a/Makefile b/Makefile
index 908a784..dccaa78 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
 PACKAGE_VERSION="0.1.11"
 CC=			gcc
 CFLAGS=		-g -Wall -O3 #-m64 #-arch ppc
-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\\\"${PACKAGE_VERSION}\\\"
+DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\\\"${PACKAGE_VERSION}\\\"
 DWGSIM_AOBJS = src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o \
 			   src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o
 DWGSIM_EVAL_AOBJS = src/dwgsim_eval.o \
diff --git a/samtools b/samtools
new file mode 160000
index 0000000..28391e5
--- /dev/null
+++ b/samtools
@@ -0,0 +1 @@
+Subproject commit 28391e5898804ce6b805016d8c676fdf61442eb3