diff --git a/buildContainers.nf b/buildContainers.nf
index 145bbde39c..ba6d96ff32 100644
--- a/buildContainers.nf
+++ b/buildContainers.nf
@@ -179,6 +179,7 @@ def defineContainersList(){
   return [
     'freebayes',
     'gatk',
+    'gatk4',
     'igvtools',
     'mutect1',
     'picard',
@@ -207,8 +208,8 @@ def helpMessage() {
   log.info "    --containers: Choose which containers to build"
   log.info "       Default: all"
   log.info "       Possible values:"
-  log.info "         all, freebayes, gatk, igvtools, mutect1, picard, qctools"
-  log.info "         r-base, runallelecount, sarek, snpeff"
+  log.info "         all, freebayes, gatk, gatk4, igvtools, mutect1, picard"
+  log.info "         qctools, r-base, runallelecount, sarek, snpeff"
   log.info "         snpeffgrch37, snpeffgrch38, vepgrch37, vepgrch38"
   log.info "    --docker: Build containers using Docker"
   log.info "    --help"
diff --git a/containers/gatk4/Dockerfile b/containers/gatk4/Dockerfile
new file mode 100644
index 0000000000..ad3cfc8aef
--- /dev/null
+++ b/containers/gatk4/Dockerfile
@@ -0,0 +1,15 @@
+FROM nfcore/base:latest
+
+LABEL \
+  author="Maxime Garcia" \
+  description="GATK4 Image for Sarek" \
+  maintainer="maxime.garcia@scilifelab.se"
+
+COPY environment.yml /
+
+RUN \
+  conda env create -f /environment.yml && \
+  conda clean -a
+
+  # Export PATH
+ENV PATH /opt/conda/envs/sarek-gatk4-2.0/bin:$PATH
diff --git a/containers/gatk4/Singularity b/containers/gatk4/Singularity
deleted file mode 100644
index 44f0259380..0000000000
--- a/containers/gatk4/Singularity
+++ /dev/null
@@ -1,19 +0,0 @@
-Bootstrap: docker
-From: ubuntu:18.04
-
-%post
-    apt-get -y update
-    apt-get -y install openjdk-8-jre-headless
-
-%help
-	Custom container for GATK4 to contain only single jar as the result of "./gradlew localJar" in /opt ; you have to change the filename for the created jar below
-
-%files
-   /home/szilva/dev/gatk/build/libs/gatk-package-4.0.4.0-15-g61c6891-SNAPSHOT-local.jar	/opt/gatk4.jar
-
-%environment
-    GATK_HOME=/opt
-    export GATK_HOME
-
-%labels
-   AUTHOR szilveszter.juhos@scilifelab.se
diff --git a/containers/gatk4/environment.yml b/containers/gatk4/environment.yml
new file mode 100644
index 0000000000..041d2a2b92
--- /dev/null
+++ b/containers/gatk4/environment.yml
@@ -0,0 +1,9 @@
+# You can use this file to create a conda environment:
+#   conda env create -f environment.yml
+name: sarek-gatk4-2.0
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - gatk4=4.0.4.0
diff --git a/scripts/do_all.sh b/scripts/do_all.sh
index c2b1f07abd..e4780958a1 100755
--- a/scripts/do_all.sh
+++ b/scripts/do_all.sh
@@ -57,8 +57,8 @@ function toLower() {
 
 if [[ $TOOL = docker ]] && [[ GRCh37,GRCh38 =~ $GENOME ]]
 then
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers freebayes,gatk,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers freebayes,gatk,gatk4,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff
     nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 else
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers freebayes,gatk,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers freebayes,gatk,gatk4,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 fi