diff --git a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf
index 46357d6fbe..2933988e22 100644
--- a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf
+++ b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf
@@ -46,9 +46,10 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK {
 
     // Convert all sample vcfs into a genomicsdb workspace using genomicsdbimport
     GATK4_GENOMICSDBIMPORT(gendb_input, false, false, false)
-
-    genotype_input = GATK4_GENOMICSDBIMPORT.out.genomicsdb.map{ meta, genomicsdb -> [ meta, genomicsdb, [], [], [] ] }
-
+    genotype_input = GATK4_GENOMICSDBIMPORT.out.genomicsdb.join(
+        GATK4_GENOMICSDBIMPORT.out.intervallist).map{
+        meta, genomicsdb, intervallist -> [ meta, genomicsdb, [], intervallist, [] ]
+    }
     // Joint genotyping performed using GenotypeGVCFs
     // Sort vcfs called by interval within each VCF