diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7f082a8c..038b7090 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Merge output from germlinecnvcaller [#635](https://github.com/nf-core/raredisease/pull/635)
 - Update tools [#623](https://github.com/nf-core/raredisease/pull/623)
 - Update output file name prefix for upd and chromograph to sample-based [#620](https://github.com/nf-core/raredisease/pull/620)
 - Update tools [#619](https://github.com/nf-core/raredisease/pull/619)
diff --git a/conf/modules/call_sv_germlinecnvcaller.config b/conf/modules/call_sv_germlinecnvcaller.config
index a63da3d3..c1efa375 100644
--- a/conf/modules/call_sv_germlinecnvcaller.config
+++ b/conf/modules/call_sv_germlinecnvcaller.config
@@ -34,4 +34,9 @@ process {
         ext.prefix = { "${meta.id}_gatkcnv_segments_refiltered" }
         ext.args = { '--output-type z --exclude "N_ALT = 0" ' }
     }
+
+    withName: '.*CALL_STRUCTURAL_VARIANTS:CALL_SV_GERMLINECNVCALLER:SVDB_MERGE_GCNVCALLER' {
+        ext.args   = '--notag --pass_only'
+        ext.prefix = { "${meta.id}_gcnvcaller" }
+    }
 }
diff --git a/conf/wes.config b/conf/wes.config
deleted file mode 100644
index b056190d..00000000
--- a/conf/wes.config
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
-========================================================================================
-    nf-core/raredisease Nextflow whole-exome sequencing (WES) config file
-========================================================================================
-    This config file is invoked when `--analysis_type` = 'wes'.
-    The purpose is to reduce the amount of resources used compared to WGS data.
-----------------------------------------------------------------------------------------
-*/
-
-process {
-    withLabel:process_medium {
-        cpus   = { check_max( 3     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 30.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
-    }
-    withLabel:process_high {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 60.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
-    }
-}
diff --git a/nextflow.config b/nextflow.config
index cb12cf84..72717041 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -283,11 +283,6 @@ podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
 
-// Load wes.config if --analysis_type='wes'
-if (params.analysis_type == 'wes') {
-    includeConfig 'conf/wes.config'
-}
-
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
 
diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf
index c7d251b9..3222c9b9 100644
--- a/subworkflows/local/call_structural_variants.nf
+++ b/subworkflows/local/call_structural_variants.nf
@@ -58,7 +58,7 @@ workflow CALL_STRUCTURAL_VARIANTS {
         }
 
         if (!params.skip_germlinecnvcaller) {
-            CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model)
+            CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model, ch_case_info)
                 .genotyped_filtered_segments_vcf
                 .collect{it[1]}
                 .set { gcnvcaller_vcf }
diff --git a/subworkflows/local/variant_calling/call_sv_cnvnator.nf b/subworkflows/local/variant_calling/call_sv_cnvnator.nf
index 995b6919..62074ecb 100644
--- a/subworkflows/local/variant_calling/call_sv_cnvnator.nf
+++ b/subworkflows/local/variant_calling/call_sv_cnvnator.nf
@@ -44,6 +44,7 @@ workflow CALL_SV_CNVNATOR {
         ch_versions = ch_versions.mix(CNVNATOR_PARTITION.out.versions)
         ch_versions = ch_versions.mix(CNVNATOR_CALL.out.versions)
         ch_versions = ch_versions.mix(CNVNATOR_CONVERT2VCF.out.versions)
+        ch_versions = ch_versions.mix(SVDB_MERGE_CNVNATOR.out.versions)
 
     emit:
         vcf        = SVDB_MERGE_CNVNATOR.out.vcf  // channel: [ val(meta), path(*.tar.gz) ]
diff --git a/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf b/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf
index 57ed2552..566bfc2e 100644
--- a/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf
+++ b/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf
@@ -8,6 +8,7 @@ include { GATK4_GERMLINECNVCALLER             } from '../../../modules/nf-core/g
 include { GATK4_POSTPROCESSGERMLINECNVCALLS   } from '../../../modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf'
 include { BCFTOOLS_VIEW                       } from '../../../modules/nf-core/bcftools/view/main'
 include { TABIX_TABIX                         } from '../../../modules/nf-core/tabix/tabix/main'
+include { SVDB_MERGE as SVDB_MERGE_GCNVCALLER } from '../../../modules/nf-core/svdb/merge/main'
 
 workflow CALL_SV_GERMLINECNVCALLER {
     take:
@@ -18,6 +19,7 @@ workflow CALL_SV_GERMLINECNVCALLER {
         ch_genome_dictionary   // channel: [mandatory][ val(meta), path(ch_dict) ]
         ch_ploidy_model        // channel: [mandatory][ path(ch_ploidy_model) ]
         ch_gcnvcaller_model    // channel: [mandatory][ path(ch_gcnvcaller_model) ]
+        ch_case_info           // channel: [mandatory] [ val(case_info) ]
 
     main:
         ch_versions = Channel.empty()
@@ -56,17 +58,29 @@ workflow CALL_SV_GERMLINECNVCALLER {
         // Filter out reference only (0/0) segments
         BCFTOOLS_VIEW (ch_segments_in , [], [], [] )
 
+        BCFTOOLS_VIEW.out.vcf
+            .collect{it[1]}
+            .toList()
+            .set { vcf_file_list }
+
+        ch_case_info
+            .combine(vcf_file_list)
+            .set { merge_input_vcfs }
+
+        SVDB_MERGE_GCNVCALLER ( merge_input_vcfs, [] )
+
         ch_versions = ch_versions.mix(GATK4_COLLECTREADCOUNTS.out.versions)
         ch_versions = ch_versions.mix(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.versions)
         ch_versions = ch_versions.mix(GATK4_GERMLINECNVCALLER.out.versions)
         ch_versions = ch_versions.mix(GATK4_POSTPROCESSGERMLINECNVCALLS.out.versions)
         ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
         ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions)
+        ch_versions = ch_versions.mix(SVDB_MERGE_GCNVCALLER.out.versions)
 
     emit:
         genotyped_intervals_vcf          = GATK4_POSTPROCESSGERMLINECNVCALLS.out.intervals  // channel: [ val(meta), path(*.vcf.gz) ]
         genotyped_segments_vcf           = GATK4_POSTPROCESSGERMLINECNVCALLS.out.segments   // channel: [ val(meta), path(*.vcf.gz) ]
-        genotyped_filtered_segments_vcf  = BCFTOOLS_VIEW.out.vcf                            // channel: [ val(meta), path(*.vcf.gz) ]
+        genotyped_filtered_segments_vcf  = SVDB_MERGE_GCNVCALLER.out.vcf                    // channel: [ val(meta), path(*.vcf.gz) ]
         denoised_vcf                     = GATK4_POSTPROCESSGERMLINECNVCALLS.out.denoised   // channel: [ val(meta), path(*.vcf.gz) ]
         versions                         = ch_versions                                      // channel: [ versions.yml ]
 }