diff --git a/.gitmodules b/.gitmodules
index 8e68abc1b..7efde0357 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -4,6 +4,7 @@
 [submodule "htslib"]
 	path = htslib
 	url = https://github.com/walaj/htslib
+        branch = develop
 [submodule "bwa"]
 	path = bwa
 	url = https://github.com/jwalabroad/bwa
diff --git a/htslib b/htslib
index 5163833ed..293a426d2 160000
--- a/htslib
+++ b/htslib
@@ -1 +1 @@
-Subproject commit 5163833ede355f8c2a6788780c55d7598279e767
+Subproject commit 293a426d2348229d3fede23d3b212c6c9bedaeb8