diff --git a/bin/concatenateVCFs.sh b/bin/concatenateVCFs.sh
index b9672abf17..7751d02719 100755
--- a/bin/concatenateVCFs.sh
+++ b/bin/concatenateVCFs.sh
@@ -84,15 +84,16 @@ then
                 tail -n +$((L+1)) ${vcf}
             done
         done
-    ) | bgzip -@${cpus} > rawcalls.vcf.gz
-    tabix rawcalls.vcf.gz
+    ) | bgzip -@${cpus} > rawcalls.unsorted.vcf.gz
 else
     VCF=$(ls no_intervals*.vcf)
-    cp $VCF rawcalls.vcf
-    bgzip -@${cpus} rawcalls.vcf
-    tabix rawcalls.vcf.gz
+    cp $VCF rawcalls.unsorted.vcf
+    bgzip -@${cpus} rawcalls.unsorted.vcf
 fi
 
+bcftools sort rawcalls.unsorted.vcf.gz | bgzip > rawcalls.vcf.gz
+tabix -p vcf rawcalls.vcf.gz
+
 set +u
 
 # Now we have the concatenated VCF file, check for WES/panel targets, and generate a subset if there is a BED provided
@@ -102,5 +103,5 @@ if [ ! -z ${targetBED+x} ]; then
     tabix ${outputFile}.gz
 else
     # Rename the raw calls as WGS results
-    for f in rawcalls*; do mv -v $f ${outputFile}${f#rawcalls.vcf}; done
+    for f in rawcalls.vcf*; do mv -v $f ${outputFile}${f#rawcalls.vcf}; done
 fi