diff --git a/modules/getvisualisations.nf b/modules/getvisualisations.nf
index dd61b33..44bc0c9 100644
--- a/modules/getvisualisations.nf
+++ b/modules/getvisualisations.nf
@@ -102,4 +102,44 @@ process GET_ARCS {
     get_arcs.R --clusters $clusters --genes $genes --breaks $breaks --output ${sample_id}
     """
 
+}
+
+process EXPORT_BEDPE {
+
+    tag "${sample_id}"
+    label 'process_low'
+
+    publishDir "${params.outdir}/igv", mode: 'copy', overwrite: true
+
+    input:
+        val(type)
+        tuple val(sample_id), path(hybrids)
+
+    output:
+        tuple val(sample_id), path("${sample_id}.${type}.bedpe.gz"), emit: bedpe
+
+    script:
+    """
+    #!/usr/bin/env Rscript
+
+    suppressPackageStartupMessages(library(data.table))
+    suppressPackageStartupMessages(library(toscatools))
+
+    hybrids.dt <- fread("$hybrids")
+    hybrids.dt <- toscatools::reorient_hybrids(hybrids.dt)
+
+    if("$type" == "hybrids") {
+        bedpe.colnames <- c("L_seqnames", "L_start", "L_end", "R_seqnames", "R_start", "R_end", "name", "total_count", "L_strand", "R_strand")
+        bedpe.dt <- hybrids.dt[, ..bedpe.colnames]
+    } else if("$type" == "clusters") {
+        bedpe.colnames <- c("L_seqnames", "L_start", "L_end", "R_seqnames", "R_start", "R_end", "name", "count", "L_strand", "R_strand")
+        bedpe.dt <- hybrids.dt[, ..bedpe.colnames]
+    }
+
+    bedpe.dt[, `:=` (L_start = L_start - 1, 
+                     R_start = R_start - 1)]
+
+    fwrite(bedpe.dt, "${sample_id}.${type}.bedpe.gz", sep = "\t", col.names = FALSE, quote = FALSE)
+    """
+
 }
\ No newline at end of file
diff --git a/workflows/getvisualisations.nf b/workflows/getvisualisations.nf
index 4cec2c9..e0d8d21 100644
--- a/workflows/getvisualisations.nf
+++ b/workflows/getvisualisations.nf
@@ -3,9 +3,11 @@
 // Specify DSL2
 nextflow.enable.dsl=2
 
-include { EXPORT_GENOMIC_BED as EXPORT_HYBRID_GENOMIC_BED; 
+include { EXPORT_GENOMIC_BED as EXPORT_HYBRIDS_GENOMIC_BED; 
           EXPORT_GENOMIC_BED as EXPORT_CLUSTERS_GENOMIC_BED;
           EXPORT_GENOMIC_BAM;
+          EXPORT_BEDPE as EXPORT_HYBRIDS_BEDPE;
+          EXPORT_BEDPE as EXPORT_CLUSTERS_BEDPE;
           GET_CONTACT_MAPS;
           GET_ARCS } from '../modules/getvisualisations.nf'
 
@@ -20,10 +22,13 @@ workflow GET_VISUALISATIONS {
         goi
 
     main:
-        EXPORT_HYBRID_GENOMIC_BED("hybrids", hybrids)
-        EXPORT_GENOMIC_BAM(EXPORT_HYBRID_GENOMIC_BED.out.bed, genome_fai.collect())
+        EXPORT_HYBRIDS_GENOMIC_BED("hybrids", hybrids)
+        EXPORT_GENOMIC_BAM(EXPORT_HYBRIDS_GENOMIC_BED.out.bed, genome_fai.collect())
         EXPORT_CLUSTERS_GENOMIC_BED("clusters", clusters)
 
+        EXPORT_HYBRIDS_BEDPE("hybrids", hybrids)
+        EXPORT_CLUSTERS_BEDPE("clusters", clusters)
+
         if(params.goi) {
 
             GET_CONTACT_MAPS(hybrids, transcript_fai.collect(), goi.collect())