diff --git a/conf/containers.config b/conf/containers.config
index 0460cb3b8..89a02d081 100755
--- a/conf/containers.config
+++ b/conf/containers.config
@@ -76,10 +76,10 @@
     container = "cmopipeline/metadataparser:0.5.9"
   }
   withName:SomaticDellyCall {
-    container = "cmopipeline/delly-bcftools:0.0.1"
+    container = "cmopipeline/delly-bcftools:0.0.3"
   }
   withName:'.*DellyCombine' {
-    container = "cmopipeline/delly-bcftools:0.0.1"
+    container = "cmopipeline/delly-bcftools:0.0.3"
   }
   withName:SomaticRunManta {
     container = "cmopipeline/strelka2-manta-bcftools-vt:2.0.1"
@@ -115,7 +115,7 @@
 //------------------- Germline pipeline
 
   withName:GermlineDellyCall {
-    container = "cmopipeline/delly-bcftools:0.0.1"
+    container = "cmopipeline/delly-bcftools:0.0.3"
   }
   withName:GermlineRunHaplotypecaller {
     container = "broadinstitute/gatk:4.1.0.0"
diff --git a/containers/delly-bcftools/Dockerfile b/containers/delly-bcftools/Dockerfile
index e09c718d1..869c0f9c1 100644
--- a/containers/delly-bcftools/Dockerfile
+++ b/containers/delly-bcftools/Dockerfile
@@ -2,12 +2,18 @@ FROM halllab/bcftools:v1.9
 
 LABEL maintainer="Anne Marie Noronha (noronhaa@mskcc.org)" \
       version.ubuntu="18.04" \
-      version.delly="0.8.2" \
-      version.htslib="1.9"
+      version.delly="1.2.6" \
+      version.htslib="1.20" \
+      version.image="0.0.3"
 
 # set the environment variables
-ENV delly_version 0.8.2
-ENV htslib_version 1.9
+ENV delly_version 1.2.6
+ENV htslib_version 1.20
+
+# APT repository has moved to archive. Sources needs to change.
+RUN sed -i /stretch-updates/d /etc/apt/sources.list
+RUN sed -i "s/security.debian/archive.debian/g" /etc/apt/sources.list
+RUN sed -i "s/deb.debian/archive.debian/g" /etc/apt/sources.list
 
 # run update
 RUN apt-get update -y && apt-get install -y \