diff --git a/deps/dozeu b/deps/dozeu
index 1a70aec5e25..c7dce486aad 160000
--- a/deps/dozeu
+++ b/deps/dozeu
@@ -1 +1 @@
-Subproject commit 1a70aec5e25fd5bcf8a8cce1e886f31d1dcc488b
+Subproject commit c7dce486aadc1f085811939d035ced2562f6c005
diff --git a/deps/gbwt b/deps/gbwt
index 029c2b45667..15ca8a18bbe 160000
--- a/deps/gbwt
+++ b/deps/gbwt
@@ -1 +1 @@
-Subproject commit 029c2b456675eab0fbb55de21c8002e1660cb0d3
+Subproject commit 15ca8a18bbe00cbc51bc80842daac8ecd3fe07a7
diff --git a/deps/gcsa2 b/deps/gcsa2
index 7dbf9305817..d246cfd5dbe 160000
--- a/deps/gcsa2
+++ b/deps/gcsa2
@@ -1 +1 @@
-Subproject commit 7dbf93058171b5af420f1b6166d4d2bf54cd8748
+Subproject commit d246cfd5dbe0d45546f28213c0245aa308bdb462
diff --git a/deps/libhandlegraph b/deps/libhandlegraph
index 8bb58a35014..c7f491fa7c9 160000
--- a/deps/libhandlegraph
+++ b/deps/libhandlegraph
@@ -1 +1 @@
-Subproject commit 8bb58a3501424ca2876287e383cd650a98608c41
+Subproject commit c7f491fa7c9b33e6ef77ffefabb640549c072ebf
diff --git a/deps/libvgio b/deps/libvgio
index 9b0d0e11df6..4d9d39cf410 160000
--- a/deps/libvgio
+++ b/deps/libvgio
@@ -1 +1 @@
-Subproject commit 9b0d0e11df6f9bd389ba4dba08d107953eabff8f
+Subproject commit 4d9d39cf410893655e2e30d49e41ea477ad8e5c4
diff --git a/deps/sublinear-Li-Stephens b/deps/sublinear-Li-Stephens
index 4efb2f3933e..5c186d151dc 160000
--- a/deps/sublinear-Li-Stephens
+++ b/deps/sublinear-Li-Stephens
@@ -1 +1 @@
-Subproject commit 4efb2f3933ea8c684fe289e8f07f626f0747436e
+Subproject commit 5c186d151dc5440d023bf0501e2b7960d1dbd80d
diff --git a/vgci/vgci.sh b/vgci/vgci.sh
index 44131e0b607..19867c70542 100755
--- a/vgci/vgci.sh
+++ b/vgci/vgci.sh
@@ -30,7 +30,7 @@ KEEP_INTERMEDIATE_FILES=0
 # Should we show stdout and stderr from tests? If so, set to "-s".
 SHOW_OPT=""
 # What toil-vg should we install?
-TOIL_VG_PACKAGE="git+https://github.com/vgteam/toil-vg.git@64774cc76ef117aef705c1b5203450482c6a4b60"
+TOIL_VG_PACKAGE="git+https://github.com/vgteam/toil-vg.git@ed7fe342713a5687ecf705e596b27aa8de6e3fe9"
 # What toil should we install?
 # Could be something like "toil[aws,mesos]==3.20.0"
 # or "git+https://github.com/DataBiosphere/toil.git@3ab74776a3adebd6db75de16985ce9d734f60743#egg=toil[aws,mesos]"