diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6f3161eb42..72195563fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [1767](https://github.com/nf-core/sarek/pull/1767) - Bump nf-schema version to 2.2.1
+- [1777](https://github.com/nf-core/sarek/pull/1777) - Merge intervals for WES in GATK GenomicsDBImport
 
 ### Fixed
 
diff --git a/conf/modules/joint_germline.config b/conf/modules/joint_germline.config
index 61a296721d..b3f5bffc8b 100644
--- a/conf/modules/joint_germline.config
+++ b/conf/modules/joint_germline.config
@@ -16,7 +16,9 @@
 process {
 
     withName: 'GATK4_GENOMICSDBIMPORT' {
-        ext.args   = { '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' }
+        ext.args   = { params.wes ?
+                            '--merge-input-intervals --genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' :
+                            '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' }
         ext.prefix = { "${meta.intervals_name}.joint" }
         publishDir = [
             enabled: false