diff --git a/conf/modules/vardictjava.config b/conf/modules/vardictjava.config
new file mode 100644
index 0000000000..9133290a07
--- /dev/null
+++ b/conf/modules/vardictjava.config
@@ -0,0 +1,36 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+        ext.when   = When to run the module.
+----------------------------------------------------------------------------------------
+*/
+
+process{
+        withName: 'VARDICTJAVA' {
+        ext.args   = { "-c 1 -S 2 -E 3 -g 4 --nosv --deldupvar -Q 10 -F 0x700 -f 0.1 -N ${meta.sample}_${meta.patient}"} //
+        ext.args2  = { "-f 0.1 -A -N ${meta.sample}_${meta.patient}" }
+        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.vardictjava" : "${meta.id}.vardictjava.${intervals.simpleName}" }
+        ext.when   = { params.tools && params.tools.split(',').contains('vardictjava') }
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/" },
+            pattern: "*{vcf.gz,vcf.gz.tbi}",
+            saveAs: { meta.num_intervals > 1 ? null : "vardictjava/${meta.id}/${it}" }
+        ]
+    }
+
+    withName: 'MERGE_VARDICTJAVA' {
+        ext.prefix = { "${meta.id}.vardictjava" }
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/vardictjava/${meta.id}/" },
+            pattern: "*{vcf.gz,vcf.gz.tbi}"
+        ]
+    }
+}
diff --git a/modules.json b/modules.json
index 26d801647b..f62cedf487 100644
--- a/modules.json
+++ b/modules.json
@@ -494,6 +494,11 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
+                    "vardictjava": {
+                        "branch": "master",
+                        "git_sha": "27e170816808aedbbac23f9a1f2c7488d4b6d342",
+                        "installed_by": ["modules"]
+                    },
                     "vcftools": {
                         "branch": "master",
                         "git_sha": "624ecdc43b72e0a45bf05d9b57215d18dcd538f8",
diff --git a/modules/nf-core/vardictjava/environment.yml b/modules/nf-core/vardictjava/environment.yml
new file mode 100644
index 0000000000..4e8905e52c
--- /dev/null
+++ b/modules/nf-core/vardictjava/environment.yml
@@ -0,0 +1,8 @@
+name: vardictjava
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::htslib=1.20
+  - bioconda::vardict-java=1.8.3
diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf
new file mode 100644
index 0000000000..6329391c83
--- /dev/null
+++ b/modules/nf-core/vardictjava/main.nf
@@ -0,0 +1,67 @@
+process VARDICTJAVA {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-731b8c4cf44d76e9aa181af565b9eee448d82a8c:edd70e76f3529411a748168f6eb1a61f29702123-0' :
+        'biocontainers/mulled-v2-731b8c4cf44d76e9aa181af565b9eee448d82a8c:edd70e76f3529411a748168f6eb1a61f29702123-0' }"
+
+    input:
+    tuple val(meta), path(bams), path(bais), path(bed)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fasta_fai)
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: '-c 1 -S 2 -E 3'
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def somatic = bams instanceof List && bams.size() == 2 ? true : false
+    def input = somatic ? "-b \"${bams[0]}|${bams[1]}\"" : "-b ${bams}"
+    def filter = somatic ? "testsomatic.R" : "teststrandbias.R"
+    def convert_to_vcf = somatic ? "var2vcf_paired.pl" : "var2vcf_valid.pl"
+    """
+    export JAVA_OPTS='"-Xms${task.memory.toMega()/4}m" "-Xmx${task.memory.toGiga()}g" "-Dsamjdk.reference_fasta=${fasta}"'
+    vardict-java \\
+        ${args} \\
+        ${input} \\
+        -th ${task.cpus} \\
+        -G ${fasta} \\
+        ${bed} \\
+    | ${filter} \\
+    | ${convert_to_vcf} \\
+        ${args2} \\
+    | bgzip ${args3} --threads ${task.cpus} > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vardict-java: \$( realpath \$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//' )
+        var2vcf_valid.pl: \$( var2vcf_valid.pl -h | sed '2!d;s/.* //' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: '-c 1 -S 2 -E 3'
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo '' | gzip > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vardict-java: \$( realpath \$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//' )
+        var2vcf_valid.pl: \$( var2vcf_valid.pl -h | sed '2!d;s/.* //' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/vardictjava/meta.yml b/modules/nf-core/vardictjava/meta.yml
new file mode 100644
index 0000000000..5c2fc921ac
--- /dev/null
+++ b/modules/nf-core/vardictjava/meta.yml
@@ -0,0 +1,70 @@
+name: "vardictjava"
+description: The Java port of the VarDict variant caller
+keywords:
+  - variant calling
+  - vcf
+  - bam
+  - snv
+  - sv
+tools:
+  - "vardictjava":
+      description: "Java port of the VarDict variant discovery program"
+      homepage: "https://github.com/AstraZeneca-NGS/VarDictJava"
+      documentation: "https://github.com/AstraZeneca-NGS/VarDictJava"
+      tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava"
+      doi: "10.1093/nar/gkw227 "
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bams:
+      type: file
+      description: One or two BAM files. Supply two BAM files to run Vardict in paired mode.
+      pattern: "*.bam"
+  - bais:
+      type: file
+      description: Index/indices of the BAM file(s)
+      pattern: "*.bai"
+  - bed:
+      type: file
+      description: BED with the regions of interest
+      pattern: "*.bed"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing fasta information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: FASTA of the reference genome
+      pattern: "*.{fa,fasta}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing fasta information
+        e.g. [ id:'test', single_end:false ]
+  - fasta_fai:
+      type: file
+      description: The index of the FASTA of the reference genome
+      pattern: "*.fai"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: VCF file output
+      pattern: "*.vcf.gz"
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/vardictjava/tests/main.nf.test b/modules/nf-core/vardictjava/tests/main.nf.test
new file mode 100644
index 0000000000..483a753a89
--- /dev/null
+++ b/modules/nf-core/vardictjava/tests/main.nf.test
@@ -0,0 +1,90 @@
+nextflow_process {
+
+    name "Test Process VARDICTJAVA"
+    script "../main.nf"
+    process "VARDICTJAVA"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vardictjava"
+
+    test("homo_sapiens - [bam, bai, bed] - fasta - fai") {
+
+        when {
+            params {
+                outdir = $outputDir
+            }
+            process {
+                """
+                input[0] = Channel.value([
+                    [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                ])
+                input[1] = [
+                    [id:"ref"],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[2] = [
+                    [id:"ref"],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+            
+            
+        }
+
+    }
+
+    test("homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai") {
+
+        when {
+            params {
+                outdir = $outputDir
+            }
+            process {
+                """
+                input[0] = Channel.value([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+                    ],
+                    [
+                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
+                    ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                ])
+                input[1] = [
+                    [id:"ref"],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[2] = [
+                    [id:"ref"],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+            
+            
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/vardictjava/tests/main.nf.test.snap b/modules/nf-core/vardictjava/tests/main.nf.test.snap
new file mode 100644
index 0000000000..c32a68b742
--- /dev/null
+++ b/modules/nf-core/vardictjava/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "homo_sapiens - [bam, bai, bed] - fasta - fai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T19:08:38.328190023"
+    },
+    "homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-04T19:08:54.416661915"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vardictjava/tests/tags.yml b/modules/nf-core/vardictjava/tests/tags.yml
new file mode 100644
index 0000000000..453c9b293a
--- /dev/null
+++ b/modules/nf-core/vardictjava/tests/tags.yml
@@ -0,0 +1,2 @@
+vardictjava:
+  - modules/nf-core/vardictjava/**
diff --git a/nextflow.config b/nextflow.config
index f9fa756dbb..929f26ef90 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -442,6 +442,7 @@ includeConfig 'conf/modules/sentieon_haplotyper_joint_germline.config'
 includeConfig 'conf/modules/strelka.config'
 includeConfig 'conf/modules/tiddit.config'
 includeConfig 'conf/modules/post_variant_calling.config'
+includeConfig 'conf/modules/vardictjava.config'
 
 //annotate
 includeConfig 'conf/modules/annotate.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 1611d58f40..04ba631301 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -111,8 +111,8 @@
                     "type": "string",
                     "fa_icon": "fas fa-toolbox",
                     "description": "Tools to use for duplicate marking, variant calling and/or for annotation.",
-                    "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Strelka\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively), and bcftools annotate (needs `--bcftools_annotation`).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.",
-                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
+                    "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Strelka\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively), VarDictJava and bcftools annotate (needs `--bcftools_annotation`).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.",
+                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vardictjava|vep)?,?)*(?<!,)$"
                 },
                 "skip_tools": {
                     "type": "string",
diff --git a/subworkflows/local/bam_variant_calling_germline_all/main.nf b/subworkflows/local/bam_variant_calling_germline_all/main.nf
index deb15527d7..5a8918af0c 100644
--- a/subworkflows/local/bam_variant_calling_germline_all/main.nf
+++ b/subworkflows/local/bam_variant_calling_germline_all/main.nf
@@ -13,6 +13,7 @@ include { BAM_VARIANT_CALLING_SENTIEON_DNASCOPE
 include { BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER                                      } from '../bam_variant_calling_sentieon_haplotyper/main'
 include { BAM_VARIANT_CALLING_MPILEUP                                                  } from '../bam_variant_calling_mpileup/main'
 include { BAM_VARIANT_CALLING_SINGLE_STRELKA                                           } from '../bam_variant_calling_single_strelka/main'
+include { BAM_VARIANT_CALLING_SINGLE_VARDICTJAVA                                       } from '../bam_variant_calling_single_vardictjava/main'
 include { BAM_VARIANT_CALLING_SINGLE_TIDDIT                                            } from '../bam_variant_calling_single_tiddit/main'
 include { SENTIEON_DNAMODELAPPLY                                                       } from '../../../modules/nf-core/sentieon/dnamodelapply/main'
 include { VCF_VARIANT_FILTERING_GATK                                                   } from '../vcf_variant_filtering_gatk/main'
@@ -67,6 +68,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     vcf_sentieon_haplotyper  = Channel.empty()
     vcf_strelka              = Channel.empty()
     vcf_tiddit               = Channel.empty()
+    vcf_vardictjava          = Channel.empty()
 
     // BCFTOOLS MPILEUP
     if (tools.split(',').contains('mpileup')) {
@@ -328,6 +330,20 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
         versions = versions.mix(BAM_VARIANT_CALLING_SINGLE_STRELKA.out.versions)
     }
 
+    // VARDICTJAVA
+    if (tools.split(',').contains('vardictjava')) {
+        BAM_VARIANT_CALLING_SINGLE_VARDICTJAVA(
+            cram,
+            dict,
+            fasta,  // TODO CHECK Do I need to remap fasta and fasta_fai to match module?
+            fasta_fai,
+            intervals
+        )
+
+        vcf_vardictjava = BAM_VARIANT_CALLING_SINGLE_VARDICTJAVA.out.vcf
+        versions = versions.mix(BAM_VARIANT_CALLING_SINGLE_VARDICTJAVA.out.versions)
+    }
+
     // TIDDIT
     if (tools.split(',').contains('tiddit')) {
         BAM_VARIANT_CALLING_SINGLE_TIDDIT(
@@ -350,7 +366,8 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
         vcf_mpileup,
         vcf_sentieon_haplotyper,
         vcf_strelka,
-        vcf_tiddit
+        vcf_tiddit,
+        vcf_vardictjava
     )
 
     emit:
@@ -366,6 +383,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     vcf_sentieon_dnascope
     vcf_sentieon_haplotyper
     vcf_tiddit
+    vcf_vardictjava
 
     versions
 }
diff --git a/subworkflows/local/bam_variant_calling_single_vardictjava/main.nf b/subworkflows/local/bam_variant_calling_single_vardictjava/main.nf
new file mode 100644
index 0000000000..3ab2b4d3a3
--- /dev/null
+++ b/subworkflows/local/bam_variant_calling_single_vardictjava/main.nf
@@ -0,0 +1,72 @@
+//
+// Vardictjava germline calling
+//
+// For all modules here:
+// A when clause condition is defined in the conf/modules.config to determine if the module should be run
+
+include { VARDICTJAVA                                  } from '../../../modules/nf-core/vardictjava/main'
+include { GATK4_MERGEVCFS  as MERGE_VARDICTJAVA        } from '../../../modules/nf-core/gatk4/mergevcfs/main'
+include { SAMTOOLS_CONVERT as CRAM_TO_BAM              } from '../../../modules/nf-core/samtools/convert/main'
+
+workflow BAM_VARIANT_CALLING_SINGLE_VARDICTJAVA {
+    take:
+    cram          // channel: [mandatory] [ meta, cram, crai ]
+    dict          // channel: [optional]  [ meta, dict ]
+    fasta         // channel: [mandatory] [ fasta ]
+    fasta_fai     // channel: [mandatory] [ fasta_fai ]
+    intervals     // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi, num_intervals ] or [ [], [], 0 ] if no intervals
+
+    main:
+    versions = Channel.empty()
+
+    // Convert cram to bam
+    cram
+    .branch {meta, cram, crai ->
+        bam:    cram.extension == "bam"
+        cram:   cram.extension == "cram"}
+        .set{ch_bam_from_cram}
+
+    CRAM_TO_BAM(
+        ch_bam_from_cram.cram,
+        fasta,
+        fasta_fai
+    )
+
+    // Combine converted bam, bai and intervals
+    ch_bam_from_cram.bam
+        .mix(CRAM_TO_BAM.out.bam.join(CRAM_TO_BAM.out.bai, failOnDuplicate: true, failOnMismatch: true))
+        .combine(intervals)
+        .map{meta, bam, bai, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], bam, bai, intervals ]}
+        .set{ ch_vardict_input}
+
+    VARDICTJAVA(
+        ch_vardict_input,
+        fasta,
+        fasta_fai
+    )
+
+    // Figuring out if there is one or more vcf(s) from the same sample
+    vcf = VARDICTJAVA.out.vcf.branch{
+        // Use meta.num_intervals to asses number of intervals
+        intervals:    it[0].num_intervals > 1
+        no_intervals: it[0].num_intervals <= 1
+    }
+
+    // Only when using intervals
+    vcf_to_merge        = vcf.intervals.map{ meta, vcf -> [ groupKey(meta, meta.num_intervals), vcf ]}.groupTuple()
+
+    MERGE_VARDICTJAVA(vcf_to_merge, dict)
+
+    // Mix intervals and no_intervals channels together
+    vcf = Channel.empty().mix(MERGE_VARDICTJAVA.out.vcf, vcf.no_intervals)
+        // add variantcaller to meta map and remove no longer necessary field: num_intervals
+        .map{ meta, vcf -> [ meta - meta.subMap('num_intervals') + [ variantcaller:'vardictjava' ], vcf ] }
+
+    versions = versions.mix(VARDICTJAVA.out.versions)
+    versions = versions.mix(MERGE_VARDICTJAVA.out.versions)
+
+    emit:
+    vcf
+
+    versions
+}
diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf
index 90307f19c2..68955447d7 100644
--- a/workflows/sarek/main.nf
+++ b/workflows/sarek/main.nf
@@ -843,6 +843,7 @@ workflow SAREK {
         vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_strelka)
         vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_tiddit)
         vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_mpileup)
+        vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_vardictjava)
         vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_TUMOR_ONLY_ALL.out.vcf_all)
         vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_SOMATIC_ALL.out.vcf_all)