diff --git a/Dockerfile b/Dockerfile
index c141760..3b67a71 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -38,4 +38,14 @@ RUN wget https://github.com/genepi/haplogrep3/releases/download/v3.2.1/haplogrep
     rm haplogrep3-3.2.1-linux.zip
 ENV PATH="/opt/haplogrep:${PATH}"
 
+WORKDIR "/opt"
+RUN wget https://github.com/jbangdev/jbang/releases/download/v0.91.0/jbang-0.91.0.zip && \
+    unzip -q jbang-*.zip && \
+    mv jbang-0.91.0 jbang  && \
+    rm jbang*.zip
+
+ENV PATH="/opt/jbang/bin:${PATH}"
+WORKDIR "/opt"
+COPY ./bin/VariantMerger.java ./
+RUN jbang export portable -O=VariantMerger.jar VariantMerger.java
 
diff --git a/bin/VariantMerger.java b/bin/VariantMerger.java
new file mode 100644
index 0000000..1d3287a
--- /dev/null
+++ b/bin/VariantMerger.java
@@ -0,0 +1,86 @@
+//usr/bin/env jbang "$0" "$@" ; exit $?
+//REPOS jcenter,genepi-maven=https://genepi.i-med.ac.at/maven
+//DEPS info.picocli:picocli:4.6.1
+//DEPS genepi:genepi-io:1.1.1
+
+import java.io.File;
+import java.util.concurrent.Callable;
+import genepi.io.table.reader.CsvTableReader;
+import genepi.io.table.writer.CsvTableWriter;
+import picocli.CommandLine;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Parameters;
+
+public class VariantMerger implements Callable<Integer> {
+
+	@Parameters(description = "Combined variants file")
+	private String file;
+
+	@Option(names = "--output", description = "Output files", required = true)
+	private String output;
+
+	@Option(names = "--indel-tag", description = "Detect indels by this tag", required = false)
+	private String tag = "INDEL";
+
+	public Integer call() throws Exception {
+
+		assert (file != null);
+		assert (output != null);
+
+		CsvTableWriter writer = new CsvTableWriter(new File(output).getAbsolutePath(), '\t', false);
+		CsvTableReader reader = new CsvTableReader(file, '\t');
+
+		int lastPos = 0;
+		String[] lastRow = null;
+		int diff = 0;
+		writer.setColumns(reader.getColumns());
+
+		while (reader.next()) {
+
+			int pos = reader.getInteger("Pos");
+			int refLength = reader.getString("Ref").length();
+			int variantlength = reader.getString("Variant").length();
+
+			// init new position
+			if (lastPos == 0 || pos == 3107 ) {
+				diff = refLength - variantlength;
+				lastPos = pos;
+				lastRow = reader.getRow();
+				continue;
+			}
+
+			if (comparePositions(lastPos, pos, diff)) {
+				writer.setRow(lastRow);
+				writer.next();
+				lastPos = 0;
+			} else {
+				// since no hit, write previous row.
+				writer.setRow(lastRow);
+				writer.next();
+				diff = refLength - variantlength;
+				lastPos = pos;
+				lastRow = reader.getRow();
+			}
+
+		}
+		writer.setRow(lastRow);
+		writer.next();
+		reader.close();
+		writer.close();
+		return 0;
+	}
+
+	public static void main(String... args) {
+		int exitCode = new CommandLine(new VariantMerger()).execute(args);
+		System.exit(exitCode);
+	}
+
+	public boolean comparePositions(int lastPos, int pos, int diff) {
+		for (int i = 0; i <= Math.abs(diff); i++) {
+			if ((lastPos + i) == pos) {
+				return true;
+			}
+		}
+		return false;
+	}
+}
diff --git a/files/mutserve.zip b/files/mutserve.zip
index 62c597c..c209cd8 100644
Binary files a/files/mutserve.zip and b/files/mutserve.zip differ
diff --git a/modules/local/annotate.nf b/modules/local/annotate.nf
index 796e375..342086a 100644
--- a/modules/local/annotate.nf
+++ b/modules/local/annotate.nf
@@ -8,9 +8,13 @@ process ANNOTATE {
     path annotation
 
     output:
-    path ("${variants_ch.baseName}_ann.txt"), emit: variants_ann_ch
+    path ("${variants_ch.baseName}.annotated.txt"), emit: variants_ann_ch
 
     """
-    java -jar /opt/mutserve/mutserve.jar annotate --input ${variants_ch} --output ${variants_ch.baseName}_ann.txt --annotation ${annotation}
+    java -jar /opt/mutserve/mutserve.jar \
+        annotate \
+        --input ${variants_ch} \
+        --output ${variants_ch.baseName}.annotated.txt \
+        --annotation ${annotation}
     """
 }
diff --git a/modules/local/contamination_detection.nf b/modules/local/contamination_detection.nf
deleted file mode 100644
index bd012f4..0000000
--- a/modules/local/contamination_detection.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-process CONTAMINATION_DETECTION {
-
-    input:
-    path variants_ch
-
-    output:
-    path ("haplocheck.html"), emit: contamination_report_ch
-    path ("haplocheck.txt"), emit: contamination_txt_ch
-    """
-    java -jar /opt/haplocheck/haplocheck.jar --out haplocheck.txt --raw ${variants_ch}
-    """
-}
\ No newline at end of file
diff --git a/modules/local/filter_variants.nf b/modules/local/filter_variants.nf
new file mode 100644
index 0000000..4c6ebf6
--- /dev/null
+++ b/modules/local/filter_variants.nf
@@ -0,0 +1,38 @@
+process FILTER_VARIANTS {
+
+    //publishDir "${params.output}", mode: 'copy'
+
+    input:
+    tuple path(vcf_file), val(method)
+
+    output:
+    path("${vcf_file.baseName}.${method}.filtered.txt"), emit: combined_methods_ch
+
+    script:
+    def vcf_name = "${vcf_file}".replaceAll('.vcf.gz', '')
+
+    """
+    echo -e "ID\tFilter\tPos\tRef\tVariant\tVariantLevel\tCoverage\tType" \
+        > ${vcf_file.baseName}.${method}.txt
+    
+    if [[ ${method} == "mutserve_fusion" ]]
+    then
+        bcftools query \
+            -f '${vcf_name}.bam\t%FILTER\t%POS\t%REF\t%ALT\t[%AF\t%DP\t%GT]\n' \
+             ${vcf_file} >> ${vcf_file.baseName}.${method}.txt
+        
+        awk -F'\t' 'NR == 1 || (length(\$4) == 1 && length(\$5) == 1)' \
+            ${vcf_file.baseName}.${method}.txt > ${vcf_file.baseName}.${method}.filtered.txt
+
+    elif [[ ${method} == "mutect2_fusion" ]]
+    then
+        bcftools query \
+            -f '${vcf_name}.bam\t%FILTER\t%POS\t%REF\t%ALT\t[%AF\t%DP]\tINDEL\n' \
+            ${vcf_file} >> ${vcf_file.baseName}.${method}.txt
+
+        awk -F'\t' 'NR == 1 || ((length(\$4) > 1 || length(\$5) > 1) && length(\$4) != length(\$5))' \
+            ${vcf_file.baseName}.${method}.txt > ${vcf_file.baseName}.${method}.filtered.txt
+    fi
+    """
+}
+
diff --git a/modules/local/haplogroup_detection.nf b/modules/local/haplogroup_detection.nf
deleted file mode 100644
index 2bf2e2b..0000000
--- a/modules/local/haplogroup_detection.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-process HAPLOGROUP_DETECTION {
-
-    publishDir "${params.output_auxiliary}", mode: 'copy'
-
-    input:
-    path variants_ch
-
-    output:
-    path ("haplogroups.txt"), emit: haplogroups_ch
-
-    """
-    java -jar /opt/haplogrep/haplogrep3.jar classify --tree phylotree-fu-rcrs@1.2 --in ${variants_ch} --out haplogroups.txt --extend-report
-    """
-}
\ No newline at end of file
diff --git a/modules/local/haplogroups_contamination.nf b/modules/local/haplogroups_contamination.nf
new file mode 100644
index 0000000..1b687d0
--- /dev/null
+++ b/modules/local/haplogroups_contamination.nf
@@ -0,0 +1,26 @@
+process HAPLOGROUPS_CONTAMINATION {
+
+    publishDir "${params.output_auxiliary}", mode: 'copy'
+
+    input:
+    path(merged_vcf_ch)
+
+    output:
+    path ("haplogroups.txt"), emit: haplogroups_ch
+    path ("haplocheck.html"), emit: contamination_report_ch
+    path ("haplocheck.txt"), emit: contamination_txt_ch
+
+    """
+    java -jar /opt/haplogrep/haplogrep3.jar \
+        classify \
+        --tree phylotree-fu-rcrs@1.2 \
+        --in ${merged_vcf_ch} \
+        --out haplogroups.txt \
+        --extend-report
+
+    java -jar /opt/haplocheck/haplocheck.jar \
+        --out haplocheck.txt \
+        --raw \
+        ${merged_vcf_ch}
+    """
+}
\ No newline at end of file
diff --git a/modules/local/index.nf b/modules/local/index.nf
index 6d4fabb..148c651 100644
--- a/modules/local/index.nf
+++ b/modules/local/index.nf
@@ -7,6 +7,7 @@ process INDEX {
 
 	"""
     samtools faidx $reference
-    samtools dict $reference -o ${reference.baseName}.dict
+    	samtools dict $reference \
+	    -o ${reference.baseName}.dict
 	"""
 }
\ No newline at end of file
diff --git a/modules/local/input_validation.nf b/modules/local/input_validation.nf
index ab50c45..9ab4139 100644
--- a/modules/local/input_validation.nf
+++ b/modules/local/input_validation.nf
@@ -13,17 +13,23 @@ process INPUT_VALIDATION {
     path("contig.txt"), emit: contig_ch
 
     """
-    csvtk concat -t ${statistics} -T -o sample_statistics.txt
-    csvtk concat -t ${mapping} -T -o sample_mappings.txt
+    csvtk concat \
+        -t ${statistics} \
+        -T -o sample_statistics.txt
+    
+    csvtk concat \
+        -t ${mapping} \
+        -T -o sample_mappings.txt
+    
     java -jar /opt/mutserve/mutserve.jar stats \
-    --input sample_statistics.txt \
-    --detection-limit ${params.detection_limit}  \
-    --reference ${params.reference}  \
-    --baseQ ${params.baseQ}\
-    --mapQ ${params.mapQ} \
-    --alignQ ${params.alignQ} \
-    --output-excluded-samples excluded_samples.txt \
-    --output-contig contig.txt \
-    --tool ${params.mode}
+        --input sample_statistics.txt \
+        --detection-limit ${params.detection_limit}  \
+        --reference ${params.reference}  \
+        --baseQ ${params.baseQ}\
+        --mapQ ${params.mapQ} \
+        --alignQ ${params.alignQ} \
+        --output-excluded-samples excluded_samples.txt \
+        --output-contig contig.txt \
+        --tool ${params.mode}
     """
 }
\ No newline at end of file
diff --git a/modules/local/merge/strategy_mutect2.nf b/modules/local/merge/strategy_mutect2.nf
new file mode 100644
index 0000000..918c229
--- /dev/null
+++ b/modules/local/merge/strategy_mutect2.nf
@@ -0,0 +1,51 @@
+process STRATEGY_MUTECT2 {
+
+    //publishDir "${params.output}", mode: 'copy'
+
+    input:
+    path bam_file
+    path reference
+    path excluded_samples
+    path fasta_index_files
+    val detected_contig
+
+    output:
+    path("${bam_file.baseName}.mutect2.filtered.txt"), emit: results
+    
+    """
+    samtools index ${bam_file}
+
+    gatk Mutect2 \
+    -R ${reference} \
+    -L ${detected_contig} \
+    --min-base-quality-score ${params.baseQ} \
+    -callable-depth 6 --max-reads-per-alignment-start 0 \
+    -I ${bam_file} \
+    -O raw.vcf.gz
+    
+    gatk FilterMutectCalls \
+    -R ${reference} \
+    --min-reads-per-strand 2 \
+    -V raw.vcf.gz \
+    -O ${bam_file.baseName}.vcf.gz
+
+     bcftools norm -m-any -f ${reference} ${bam_file.baseName}.vcf.gz -o ${bam_file.baseName}.filtered.vcf.gz -Oz
+
+tabix ${bam_file.baseName}.filtered.vcf.gz
+    gatk LeftAlignAndTrimVariants \
+   -R ${reference}  \
+   -V ${bam_file.baseName}.vcf.gz \
+   -O ${bam_file.baseName}.filtered2.vcf.gz \
+   --max-indel-length 208
+
+    rm raw.vcf.gz
+
+    echo -e "ID\tFilter\tPos\tRef\tVariant\tVariantLevel\tCoverage\tType" > ${bam_file.baseName}.mutect2.txt
+
+    bcftools query -f '${bam_file}\t%FILTER\t%POS\t%REF\t%ALT\t[%AF\t%DP]\t0\n'  ${bam_file.baseName}.filtered2.vcf.gz >> ${bam_file.baseName}.mutect2.txt
+
+    awk -F'\t' 'NR == 1 || length(\$4) > 1 || length(\$5) > 1' ${bam_file.baseName}.mutect2.txt > ${bam_file.baseName}.mutect2.filtered.txt
+
+
+    """
+}
\ No newline at end of file
diff --git a/modules/local/merging_variants.nf b/modules/local/merging_variants.nf
new file mode 100644
index 0000000..d13e8c9
--- /dev/null
+++ b/modules/local/merging_variants.nf
@@ -0,0 +1,29 @@
+process MERGING_VARIANTS {
+
+    input:
+    path variants_txt
+    val mode
+
+    output:
+    path("variants.txt"), emit: txt_summarized_ch
+
+    """
+    csvtk concat \
+        -t ${variants_txt} \
+        -T -o variants.concat.txt
+    
+    csvtk sort \
+        -t variants.concat.txt \
+        -k ID:N -k Pos:n -k Type:r \
+        -T -o variants.sorted.txt
+
+    if [[ ${mode} == "fusion" ]]
+    then
+        java -jar /opt/VariantMerger.jar \
+            variants.sorted.txt \
+            --output variants.txt
+    else
+        mv variants.sorted.txt variants.txt
+    fi
+    """
+}
\ No newline at end of file
diff --git a/modules/local/mutect2.nf b/modules/local/mutect2.nf
index 0e0b690..c51f4f7 100644
--- a/modules/local/mutect2.nf
+++ b/modules/local/mutect2.nf
@@ -1,7 +1,5 @@
 process MUTECT2 {
 
-    publishDir "${params.output}", mode: 'copy'
-
     input:
     path bam_file
     path reference
@@ -10,33 +8,45 @@ process MUTECT2 {
     val detected_contig
 
     output:
-    path("${bam_file.baseName}.vcf.gz"), emit: vcf_ch
-    path("${bam_file.baseName}.txt"), emit: txt_ch
+    path("${bam_file.baseName}.txt"), emit: mutect2_txt_ch
+    tuple path("${bam_file.baseName}.vcf.gz"), val('mutect2_fusion'), emit: mutect2_fusion_vcf_ch
+    path("${bam_file.baseName}.vcf.gz"), emit: mutect2_vcf_ch
+    path("${bam_file.baseName}.vcf.gz.tbi"), emit: mutect2_vcf_idx_ch
 
     """
     samtools index ${bam_file}
 
     gatk Mutect2 \
-    --mitochondria-mode \
-    -R ${reference} \
-    -L ${detected_contig} \
-    --min-base-quality-score ${params.baseQ} \
-    -I ${bam_file} \
-    -O raw.vcf.gz
+        -R ${reference} \
+        -L ${detected_contig} \
+        --min-base-quality-score ${params.baseQ} \
+        -callable-depth 6 --max-reads-per-alignment-start 0 \
+        -I ${bam_file} \
+        -O raw.vcf.gz
     
     gatk FilterMutectCalls \
-    --mitochondria-mode \
-    --max-alt-allele-count 10 \
-    -R ${reference} \
-    --min-allele-fraction ${params.detection_limit} \
-    -V raw.vcf.gz \
-    -O ${bam_file.baseName}.vcf.gz
+        -R ${reference} \
+        --min-reads-per-strand 2 \
+        -V raw.vcf.gz \
+        -O ${bam_file.baseName}.vcf.gz
+
+    bcftools norm \
+        -m-any \
+        -f ${reference} \
+        -o ${bam_file.baseName}.norm.vcf.gz -Oz \
+        ${bam_file.baseName}.vcf.gz 
+    
+    mv ${bam_file.baseName}.norm.vcf.gz ${bam_file.baseName}.vcf.gz
+    tabix -f ${bam_file.baseName}.vcf.gz
 
+    #required for mutect2-only mode!
+    echo -e "ID\tFilter\tPos\tRef\tVariant\tVariantLevel\tCoverage\tType" \
+        > ${bam_file.baseName}.txt
+    
+    bcftools query \
+        -f '${bam_file}\t%FILTER\t%POS\t%REF\t%ALT\t[%AF\t%DP]\tMUTECT2\n' \
+        ${bam_file.baseName}.vcf.gz >> ${bam_file.baseName}.txt
+    
     rm raw.vcf.gz
-
-    echo -e "ID\tFilter\tPos\tRef\tVariant\tVariantLevel\tCoverage\tType" > ${bam_file.baseName}.txt
-
-    bcftools query -f '${bam_file}\t%FILTER\t%POS\t%REF\t%ALT\t[%AF\t%DP]\t0\n' ${bam_file.baseName}.vcf.gz >> ${bam_file.baseName}.txt
-
     """
 }
\ No newline at end of file
diff --git a/modules/local/mutect2_summarize.nf b/modules/local/mutect2_summarize.nf
deleted file mode 100644
index dcd4316..0000000
--- a/modules/local/mutect2_summarize.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-process MUTECT2_SUMMARIZE {
-
-    input:
-    path variants_txt
-
-    output:
-    path("variants.txt"), emit: txt_summarized_ch
-
-    """
-    csvtk concat -t ${variants_txt} -T -o variants.txt
-    """
-}
\ No newline at end of file
diff --git a/modules/local/mutserve.nf b/modules/local/mutserve.nf
index fa8a048..b9d6724 100644
--- a/modules/local/mutserve.nf
+++ b/modules/local/mutserve.nf
@@ -1,34 +1,42 @@
 process MUTSERVE {
 
-    publishDir "${params.output}", mode: 'copy',pattern: '*.vcf.gz'
-
     input:
-    path bam_files_ch
+    path bam_file
     path reference
     path excluded_samples
 
     output:
-    path("variants.vcf.gz"), emit: vcf_ch
-    path("variants.txt"), emit: txt_ch
-
+    path("${bam_file.simpleName}.txt"), emit: mutserve_txt_ch
+    tuple path("${bam_file.baseName}.vcf.gz"), val('mutserve_fusion'), emit: mutserve_fusion_vcf_ch
+    path("${bam_file.baseName}.vcf.gz"), emit: mutserve_vcf_ch
+    path("${bam_file.baseName}.vcf.gz.tbi"), emit: mutserve_vcf_idx_ch
+    
     script:
     def avail_mem = 1024
-    if (!task.memory) {
-        log.info '[MUTSERVE] Available memory not known - defaulting to 1GB. Specify process memory requirements to change this.'
-    } else {
+    if (task.memory) {
         avail_mem = (task.memory.mega*0.8).intValue()
     }    
 
     """
-    java -Xmx${avail_mem}M -jar /opt/mutserve/mutserve.jar call \
-    --level ${params.detection_limit} \
-    --reference ${reference} \
-    --mapQ ${params.mapQ} \
-    --baseQ ${params.baseQ} \
-    --deletions --output variants.vcf.gz \
-    --no-ansi ${bam_files_ch} \
-    --excluded-samples ${excluded_samples} \
-    --threads ${task.cpus} \
-    --write-raw
+    java -Xmx${avail_mem}M -jar /opt/mutserve/mutserve.jar \
+        call \
+        --level ${params.detection_limit} \
+        --reference ${reference} \
+        --mapQ ${params.mapQ} \
+        --baseQ ${params.baseQ} \
+        --output ${bam_file.baseName}.vcf.gz \
+        --no-ansi \
+        --excluded-samples ${excluded_samples} \
+        --write-raw \
+        ${bam_file} 
+
+    bcftools norm \
+        -m-any \
+        -f ${reference} \
+        -o ${bam_file.baseName}.norm.vcf.gz -Oz \
+        ${bam_file.baseName}.vcf.gz 
+    
+    mv ${bam_file.baseName}.norm.vcf.gz ${bam_file.baseName}.vcf.gz
+    tabix -f ${bam_file.baseName}.vcf.gz
     """
 }
\ No newline at end of file
diff --git a/modules/local/quality_control.nf b/modules/local/quality_control.nf
index 9a813b0..a084c5d 100644
--- a/modules/local/quality_control.nf
+++ b/modules/local/quality_control.nf
@@ -1,12 +1,15 @@
 process QUALITY_CONTROL {
+    
     publishDir "${params.output_reports}", mode: "copy", pattern: '*.html'
+    
     input:
     path excluded_samples
     path zip
+    
     output:
 	path "*.html"
 
 	"""
-	 multiqc . 
+	multiqc . 
 	"""
 }
\ No newline at end of file
diff --git a/modules/local/vcf_merge.nf b/modules/local/vcf_merge.nf
new file mode 100644
index 0000000..577e963
--- /dev/null
+++ b/modules/local/vcf_merge.nf
@@ -0,0 +1,19 @@
+process VCF_MERGE {
+
+    input:
+    path(variants_ch)
+    path(variants_idx_ch)
+    val count
+
+    output:
+    path ("merged.vcf.gz"), emit: vcf_merged_ch
+
+    """
+    if [[ ${count} > 1 ]]
+    then
+        bcftools merge -Oz -o merged.vcf.gz ${variants_ch} 
+    else
+        mv ${variants_ch} merged.vcf.gz 
+    fi
+    """
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index cac9dcf..b5ff855 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,7 +16,7 @@ params {
     project_date           = "`date`"
     files                  = null    
     reference              = "rcrs"
-    mode                   = "mutserve"
+    mode                   = "fusion"
     detection_limit        = 0.01    
     mapQ                   = 20
     baseQ                  = 20
diff --git a/reports/report.Rmd b/reports/report.Rmd
index b55b532..349262d 100644
--- a/reports/report.Rmd
+++ b/reports/report.Rmd
@@ -230,12 +230,21 @@ Row
 
 
 ```{r echo=FALSE, results='asis'}
+variants <- variants %>%
+  mutate(Type = case_when(
+    Type == "0/1" ~ "2",
+    Type == "1/0" ~ "2",
+    Type == "INDEL" ~ "3",
+    TRUE ~ as.character(Type)
+  ))
+
 summary_data <- aggregate(  Sample_Label ~ Pos + Type , data = variants, FUN = length)
-summary_data <- summary_data %>% filter(Sample_Label >= 2)
+summary_data <- summary_data %>% filter(Sample_Label >= 1)
 summary_data <- summary_data %>% mutate(
   label = case_when(
     Type == 1 ~ "Variant",
     Type == 2 ~ "Heteroplasmy",
+    Type == 3 ~ "INDEL",
     TRUE ~ "Unknown"
   )
 )
diff --git a/tests/data/bam/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123_copy.bam b/tests/data/bam/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123_copy.bam
deleted file mode 100644
index 5584359..0000000
Binary files a/tests/data/bam/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123_copy.bam and /dev/null differ
diff --git a/tests/mitocalling.nf.test b/tests/mitocalling.nf.test
index 4f9409e..0e62264 100644
--- a/tests/mitocalling.nf.test
+++ b/tests/mitocalling.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-            assert snapshot(path("${launchDir}/out/variants_ann.txt")).match()
+            assert snapshot(path("${launchDir}/out/variants.annotated.txt")).match()
         }
 
     }
@@ -37,7 +37,7 @@ nextflow_pipeline {
         }
 
         then {
-            assert snapshot(path("${launchDir}/out/variants_ann.txt")).match()
+            assert snapshot(path("${launchDir}/out/variants.annotated.txt")).match()
         }
 
     }
@@ -57,8 +57,7 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-            //TODO: sort variants file by sample after merging to get a deterministic order
-            //assert snapshot(path("${launchDir}/out/variants_ann.txt")).match()
+            assert snapshot(path("${launchDir}/out/variants.annotated.txt")).match()
         }
 
     }
diff --git a/tests/mitocalling.nf.test.snap b/tests/mitocalling.nf.test.snap
index 5efd4e5..d2c86c3 100644
--- a/tests/mitocalling.nf.test.snap
+++ b/tests/mitocalling.nf.test.snap
@@ -1,14 +1,20 @@
 {
+    "Runs with single BAM file and mutect2": {
+        "content": [
+            "variants.annotated.txt:md5,94fa4b4d0613f61410618a7eba4c5c97"
+        ],
+        "timestamp": "2024-02-26T23:09:58.251860914"
+    },
     "Runs with single BAM file and mutserve": {
         "content": [
-            "variants_ann.txt:md5,1d8423fc3e89a12e226e5e4b89f60150"
+            "variants.annotated.txt:md5,21b561f9b05098cdc137f43b4988570e"
         ],
-        "timestamp": "2024-01-10T14:27:36.082310248"
+        "timestamp": "2024-02-26T23:02:15.242706827"
     },
     "Runs with BAM file including different header contigs": {
         "content": [
-            "variants_ann.txt:md5,c2aa6c45193a921f4a20238fe9bf6cd8"
+            "variants.annotated.txt:md5,d68e6fed173c766228164438a24ecf5a"
         ],
-        "timestamp": "2024-01-10T14:28:13.798945731"
+        "timestamp": "2024-02-26T23:03:07.470112898"
     }
 }
\ No newline at end of file
diff --git a/tests/data/test_single_bam.config b/tests/test_mitohpc_fusion.config
similarity index 75%
rename from tests/data/test_single_bam.config
rename to tests/test_mitohpc_fusion.config
index f2f23c1..433f8a8 100644
--- a/tests/data/test_single_bam.config
+++ b/tests/test_mitohpc_fusion.config
@@ -10,7 +10,9 @@
 
 params {
     project         = "test-job"
-    files           = "$projectDir/tests/data/bam/*.bam"
-    output          = "out"
+    files           = "$projectDir/tests/data/bam/mitohpc/*.bam"
+    output          = "output/mitohpc_fusion"
+    detection_limit = 0.03    
+    mode            = "fusion"
 }
 
diff --git a/tests/data/mutect2_test_single_bam.config b/tests/test_mitohpc_mutect2.config
similarity index 75%
rename from tests/data/mutect2_test_single_bam.config
rename to tests/test_mitohpc_mutect2.config
index 42b6371..8948f23 100644
--- a/tests/data/mutect2_test_single_bam.config
+++ b/tests/test_mitohpc_mutect2.config
@@ -9,9 +9,10 @@
 */
 
 params {
-    project         = "test-job-mutect2"
-    files           = "$projectDir/tests/data/bam/*.bam"
-    output          = "out"
+    project         = "test-job"
+    files           = "$projectDir/tests/data/bam/mitohpc/*.bam"
+    output          = "output/mitohpc_mutect2"
+    detection_limit = 0.03    
     mode            = "mutect2"
 }
 
diff --git a/tests/test_mitohpc_mutserve.config b/tests/test_mitohpc_mutserve.config
new file mode 100644
index 0000000..6c93272
--- /dev/null
+++ b/tests/test_mitohpc_mutserve.config
@@ -0,0 +1,18 @@
+/*
+========================================================================================
+    Nextflow config file for running minimal tests
+========================================================================================
+    Defines input files and everything required to run a fast and simple pipeline test.
+    Use as follows:
+        nextflow run main.nf -profile test,development
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    project         = "test-job"
+    files           = "$projectDir/tests/data/bam/mitohpc/*.bam"
+    output          = "output/mitohpc_mutserve"
+    detection_limit = 0.03    
+    mode            = "mutserve"
+}
+
diff --git a/workflows/mtdna_server_2.nf b/workflows/mtdna_server_2.nf
index 16cc366..a05525c 100644
--- a/workflows/mtdna_server_2.nf
+++ b/workflows/mtdna_server_2.nf
@@ -21,14 +21,14 @@ include { INPUT_VALIDATION } from '../modules/local/input_validation'
 include { QUALITY_CONTROL } from '../modules/local/quality_control'
 include { MUTSERVE } from '../modules/local/mutserve'
 include { MUTECT2 } from '../modules/local/mutect2'
-include { MUTECT2_SUMMARIZE } from '../modules/local/mutect2_summarize'
+include { FILTER_VARIANTS } from '../modules/local/filter_variants'
+include { MERGING_VARIANTS } from '../modules/local/merging_variants'
+include { VCF_MERGE } from '../modules/local/vcf_merge'
 include { ANNOTATE } from '../modules/local/annotate'
-include { HAPLOGROUP_DETECTION } from '../modules/local/haplogroup_detection'
-include { CONTAMINATION_DETECTION } from '../modules/local/contamination_detection'
+include { HAPLOGROUPS_CONTAMINATION } from '../modules/local/haplogroups_contamination'
 include { REPORT } from '../modules/local/report'
 
 
-
 workflow MTDNA_SERVER_2 {
  
     report_file_ch = file("$projectDir/reports/report.Rmd")
@@ -65,45 +65,98 @@ workflow MTDNA_SERVER_2 {
 
     haplogrep_ch = file("$projectDir/files/haplogroups.txt")
     contamination_ch = file("$projectDir/files/haplocheck.txt")
-    if (params.mode == 'mutect2') {
+
+    if (params.mode == 'mutserve') {
+
+        MUTSERVE(
+            bams_ch,
+            ref_file_mutserve,
+            INPUT_VALIDATION.out.excluded_ch
+        )
+
+        MERGING_VARIANTS(
+            MUTSERVE.out.mutserve_txt_ch.collect(),
+            params.mode
+        )
+
+        variants_txt_ch = MERGING_VARIANTS.out.txt_summarized_ch
+        variants_vcf_ch = MUTSERVE.out.mutserve_vcf_ch.collect()
+        variants_vcf_idx_ch = MUTSERVE.out.mutserve_vcf_idx_ch.collect()
+        file_count =  MUTSERVE.out.mutserve_vcf_ch.count()
+       
+    } 
+
+    else if (params.mode == 'mutect2') {
 
         MUTECT2(
-        bams_ch,
-        ref_file_mutect2,
-        INPUT_VALIDATION.out.excluded_ch,
-        INDEX.out.fasta_index_ch,
-        detected_contig
+            bams_ch,
+            ref_file_mutect2,
+            INPUT_VALIDATION.out.excluded_ch,
+            INDEX.out.fasta_index_ch,
+            detected_contig
         )
 
-        MUTECT2_SUMMARIZE(
-        MUTECT2.out.txt_ch.collect()
+        MERGING_VARIANTS(
+            MUTECT2.out.mutect2_txt_ch.collect(),
+            params.mode
         )
 
-        variants_txt_ch = MUTECT2_SUMMARIZE.out.txt_summarized_ch
+        variants_txt_ch = MERGING_VARIANTS.out.txt_summarized_ch
+        variants_vcf_ch = MUTECT2.out.mutect2_vcf_ch.collect()
+        variants_vcf_idx_ch = MUTECT2.out.mutect2_vcf_idx_ch.collect()
+        file_count =  MUTECT2.out.mutect2_vcf_ch.count()
     }
 
-    else {
+    else if (params.mode == 'fusion') {
 
         MUTSERVE(
-            bams_ch.collect(),
+            bams_ch,
             ref_file_mutserve,
             INPUT_VALIDATION.out.excluded_ch
         )
 
-        variants_txt_ch = MUTSERVE.out.txt_ch
+        MUTECT2(
+            bams_ch,
+            ref_file_mutect2,
+            INPUT_VALIDATION.out.excluded_ch,
+            INDEX.out.fasta_index_ch,
+            detected_contig
+        )
+        
+        merged_ch = MUTSERVE.out.mutserve_fusion_vcf_ch.concat(MUTECT2.out.mutect2_fusion_vcf_ch)
 
-        HAPLOGROUP_DETECTION(
-            MUTSERVE.out.vcf_ch
-        )    
+        FILTER_VARIANTS (
+            merged_ch
+        )
 
-        haplogrep_ch = HAPLOGROUP_DETECTION.out.haplogroups_ch
-       
-        CONTAMINATION_DETECTION(
-            MUTSERVE.out.vcf_ch
+        MERGING_VARIANTS(
+            FILTER_VARIANTS.out.combined_methods_ch.collect(),
+            params.mode
         )
 
-         contamination_ch =  CONTAMINATION_DETECTION.out.contamination_txt_ch
-    } 
+        variants_txt_ch = MERGING_VARIANTS.out.txt_summarized_ch
+        // only use mutserve calls for haplogroup and contamination detection
+        variants_vcf_ch = MUTSERVE.out.mutserve_vcf_ch.collect()
+        variants_vcf_idx_ch = MUTSERVE.out.mutserve_vcf_idx_ch.collect()
+        file_count =  MUTSERVE.out.mutserve_vcf_ch.count()
+    }
+
+    VCF_MERGE (
+        variants_vcf_ch,
+        variants_vcf_idx_ch,
+        file_count
+        )
+
+    if (params.mode != 'mutect2') {
+        HAPLOGROUPS_CONTAMINATION (
+            VCF_MERGE.out.vcf_merged_ch
+        )
+        haplogrep_ch = HAPLOGROUPS_CONTAMINATION.out.haplogroups_ch
+        contamination_ch =  HAPLOGROUPS_CONTAMINATION.out.contamination_txt_ch
+        
+    }
+
+
 
     ANNOTATE(
         variants_txt_ch,
@@ -124,10 +177,7 @@ workflow MTDNA_SERVER_2 {
 }
 
 workflow.onComplete {
-    //TODO: use templates
-    //TODO: move in EmailHelper class
-    //see https://www.nextflow.io/docs/latest/mail.html for configuration etc...
-   
+  
     def report = new CloudgeneReport()
    
     //job failed