diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6db667ce..fef1c805 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,7 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- Restrict deepvariant analysis of WES samples to bait regions [#633](https://github.com/nf-core/raredisease/pull/633)
+- Restrict deepvariant analysis of WES samples to bait regions [#633](https://github.com/nf-core/raredisease/pull/633), [#658](https://github.com/nf-core/raredisease/pull/658)
 - bcftools annotate declaration in annotate CADD subworkflow [#624](https://github.com/nf-core/raredisease/pull/624)
 - Rhocallviz subworkflow will only be invocated once per sample [#621](https://github.com/nf-core/raredisease/pull/621)
 - Updated createCaseChannel function to include a check for maternal and paternal ids being set to a numeric 0 [#643](https://github.com/nf-core/raredisease/pull/643)
diff --git a/CITATIONS.md b/CITATIONS.md
index c28f2ec2..27a30628 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -16,6 +16,10 @@
 
   > Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008
 
+- [BEDTools](https://academic.oup.com/bioinformatics/article/26/6/841/244688)
+
+  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841-842. doi:10.1093/bioinformatics/btq033
+
 - [BWA-MEM](https://arxiv.org/abs/1303.3997)
 
   > Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Published online May 26, 2013. Accessed March 14, 2023. http://arxiv.org/abs/1303.3997
diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config
index 89a2a1eb..894b5959 100644
--- a/conf/modules/prepare_references.config
+++ b/conf/modules/prepare_references.config
@@ -104,6 +104,16 @@ process {
         ext.args2 = '--csi'
     }
 
+    withName: '.*PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED' {
+        ext.when   = { !params.target_bed.equals(null) && params.bait_padding > 0 }
+        ext.prefix = { "${meta.id}_pad${params.bait_padding}" }
+        ext.args   = { "-b ${params.bait_padding}" }
+    }
+
+    withName: '.*PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED' {
+        ext.prefix = { "${meta.id}_pad${params.bait_padding}" }
+    }
+
     withName: '.*PREPARE_REFERENCES:GATK_BILT' {
         ext.when = { !params.target_bed.equals(null) }
         ext.prefix = { "${meta.id}_target" }
diff --git a/modules.json b/modules.json
index ad388fcf..82de9d5b 100644
--- a/modules.json
+++ b/modules.json
@@ -55,6 +55,11 @@
                         "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963",
                         "installed_by": ["modules"]
                     },
+                    "bedtools/slop": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "bwa/index": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
diff --git a/modules/nf-core/bedtools/slop/environment.yml b/modules/nf-core/bedtools/slop/environment.yml
new file mode 100644
index 00000000..5683bc05
--- /dev/null
+++ b/modules/nf-core/bedtools/slop/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bedtools=2.31.1
diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf
new file mode 100644
index 00000000..e5b8e1ef
--- /dev/null
+++ b/modules/nf-core/bedtools/slop/main.nf
@@ -0,0 +1,49 @@
+process BEDTOOLS_SLOP {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' :
+        'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }"
+
+    input:
+    tuple val(meta), path(bed)
+    path  sizes
+
+    output:
+    tuple val(meta), path("*.bed"), emit: bed
+    path  "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$bed" == "${prefix}.bed") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    bedtools \\
+        slop \\
+        -i $bed \\
+        -g $sizes \\
+        $args \\
+        > ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bedtools/slop/meta.yml b/modules/nf-core/bedtools/slop/meta.yml
new file mode 100644
index 00000000..762db534
--- /dev/null
+++ b/modules/nf-core/bedtools/slop/meta.yml
@@ -0,0 +1,51 @@
+name: bedtools_slop
+description: Adds a specified number of bases in each direction (unique values may
+  be specified for either -l or -r)
+keywords:
+  - bed
+  - slopBed
+  - bedtools
+tools:
+  - bedtools:
+      description: |
+        A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
+      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
+      licence: ["MIT"]
+      identifier: biotools:bedtools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Input BED file
+        pattern: "*.{bed}"
+  - - sizes:
+        type: file
+        description: Chromosome sizes file
+output:
+  - bed:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bed":
+          type: file
+          description: Slopped BED file
+          pattern: "*.{bed}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@edmundmiller"
+  - "@sruthipsuresh"
+  - "@drpatelh"
+maintainers:
+  - "@edmundmiller"
+  - "@sruthipsuresh"
+  - "@drpatelh"
diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test b/modules/nf-core/bedtools/slop/tests/main.nf.test
new file mode 100644
index 00000000..c8dccc8e
--- /dev/null
+++ b/modules/nf-core/bedtools/slop/tests/main.nf.test
@@ -0,0 +1,36 @@
+
+nextflow_process {
+
+    name "Test Process BEDTOOLS_SLOP"
+    script "../main.nf"
+    process "BEDTOOLS_SLOP"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bedtools"
+    tag "bedtools/slop"
+
+    test("test-bedtools-slop") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test.snap b/modules/nf-core/bedtools/slop/tests/main.nf.test.snap
new file mode 100644
index 00000000..899ac21b
--- /dev/null
+++ b/modules/nf-core/bedtools/slop/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "test-bedtools-slop": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bed:md5,4f1d8924925fe5d205c9e1981fe290a4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bed:md5,4f1d8924925fe5d205c9e1981fe290a4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:52:04.945029"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/slop/tests/nextflow.config b/modules/nf-core/bedtools/slop/tests/nextflow.config
new file mode 100644
index 00000000..fef75481
--- /dev/null
+++ b/modules/nf-core/bedtools/slop/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: BEDTOOLS_SLOP {
+        ext.args = '-l 15 -r 30'
+        ext.prefix = { "${meta.id}_out" }
+    }
+}
diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf
index 99b291c9..2ea912a1 100644
--- a/subworkflows/local/prepare_references.nf
+++ b/subworkflows/local/prepare_references.nf
@@ -2,6 +2,7 @@
 // Prepare reference files
 //
 
+include { BEDTOOLS_SLOP as BEDTOOLS_PAD_TARGET_BED           } from '../../modules/nf-core/bedtools/slop/main'
 include { BWA_INDEX as BWA_INDEX_GENOME                      } from '../../modules/nf-core/bwa/index/main'
 include { BWA_INDEX as BWA_INDEX_MT                          } from '../../modules/nf-core/bwa/index/main'
 include { BWA_INDEX as BWA_INDEX_MT_SHIFT                    } from '../../modules/nf-core/bwa/index/main'
@@ -24,6 +25,7 @@ include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME      } from '../../modul
 include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT          } from '../../modules/nf-core/sentieon/bwaindex/main'
 include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT    } from '../../modules/nf-core/sentieon/bwaindex/main'
 include { TABIX_BGZIPTABIX as TABIX_PBT                      } from '../../modules/nf-core/tabix/bgziptabix/main'
+include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_PADDED_BED    } from '../../modules/nf-core/tabix/bgziptabix/main'
 include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_VCFANNOEXTRA  } from '../../modules/nf-core/tabix/bgziptabix/main'
 include { TABIX_TABIX as TABIX_VCFANNOEXTRA                  } from '../../modules/nf-core/tabix/tabix/main'
 include { TABIX_TABIX as TABIX_DBSNP                         } from '../../modules/nf-core/tabix/tabix/main'
@@ -97,8 +99,18 @@ workflow PREPARE_REFERENCES {
         // Vcf, tab and bed indices
         TABIX_DBSNP(ch_known_dbsnp)
         TABIX_GNOMAD_AF(ch_gnomad_af_tab)
-        TABIX_PT(ch_target_bed).tbi.set { ch_tbi }
-        TABIX_PBT(ch_target_bed).gz_tbi.set { ch_bgzip_tbi }
+
+        // Index target bed file in case of gz input
+        TABIX_PT(ch_target_bed)
+        ch_target_bed
+            .join(TABIX_PT.out.tbi)
+            .set{ ch_trgt_bed_tbi }
+        // Compress and index target bed file in case of uncompressed input
+        TABIX_PBT(ch_target_bed).gz_tbi
+            .set { ch_bgzip_tbi }
+        ch_target_bed_gz_tbi = Channel.empty()
+            .mix(ch_trgt_bed_tbi, ch_bgzip_tbi)
+
         ch_vcfanno_extra_unprocessed
             .branch { it ->
                 bgzipindex: !it[1].toString().endsWith(".gz")
@@ -121,6 +133,15 @@ workflow PREPARE_REFERENCES {
             .mix(ch_vcfanno_bgzip, ch_vcfanno_index)
             .collect()
             .set{ch_vcfanno_extra}
+
+        // Pad bed file
+        BEDTOOLS_PAD_TARGET_BED(
+            ch_target_bed,
+            ch_fai.map { _meta, fai -> return fai }
+        )
+        TABIX_BGZIPINDEX_PADDED_BED(BEDTOOLS_PAD_TARGET_BED.out.bed).gz_tbi
+            .set { ch_target_bed_gz_tbi }
+
         // Generate bait and target intervals
         GATK_BILT(ch_target_bed, ch_dict).interval_list
         GATK_ILT(GATK_BILT.out.interval_list)
@@ -163,6 +184,8 @@ workflow PREPARE_REFERENCES {
         ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.versions)
         ch_versions = ch_versions.mix(TABIX_VCFANNOEXTRA.out.versions)
         ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions)
+        ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions)
+        ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_PADDED_BED.out.versions)
         ch_versions = ch_versions.mix(GATK_BILT.out.versions)
         ch_versions = ch_versions.mix(GATK_ILT.out.versions)
         ch_versions = ch_versions.mix(CAT_CAT_BAIT.out.versions)
@@ -190,10 +213,9 @@ workflow PREPARE_REFERENCES {
         mtshift_fasta         = GATK_SHIFTFASTA.out.shift_fa.collect()                                       // channel: [ val(meta), path(fasta) ]
         mtshift_bwa_index     = ch_bwa_mtshift                                                               // channel: [ val(meta), path(index) ]
         mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT.out.index.collect()                                   // channel: [ val(meta), path(index) ]
-
         gnomad_af_idx         = TABIX_GNOMAD_AF.out.tbi.collect()                                            // channel: [ val(meta), path(fasta) ]
         known_dbsnp_tbi       = TABIX_DBSNP.out.tbi.collect()                                                // channel: [ val(meta), path(fasta) ]
-        target_bed            = Channel.empty().mix(ch_tbi, ch_bgzip_tbi).collect()                          // channel: [ val(meta), path(bed), path(tbi) ]
+        target_bed            = ch_target_bed_gz_tbi.collect()                                               // channel: [ val(meta), path(bed), path(tbi) ]
         vcfanno_extra         = ch_vcfanno_extra.ifEmpty([[]])                                               // channel: [ [path(vcf), path(tbi)] ]
         bait_intervals        = CAT_CAT_BAIT.out.file_out.map{ meta, inter -> inter}.collect().ifEmpty([[]]) // channel: [ path(intervals) ]
         target_intervals      = GATK_BILT.out.interval_list.map{ meta, inter -> inter}.collect()             // channel: [ path(interval_list) ]
diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
index 00a176ab..24e7ed73 100644
--- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
@@ -302,6 +302,7 @@ def toolCitationText() {
     ]
     other_citation_text = [
         "BCFtools (Danecek et al., 2021),",
+        "BEDTools (Quinlan & Hall, 2010),",
         "GATK (McKenna et al., 2010),",
         "MultiQC (Ewels et al. 2016),",
         params.skip_peddy     ? "" : "Peddy (Pedersen & Quinlan, 2017),",
@@ -432,7 +433,8 @@ def toolBibliographyText() {
         params.run_rtgvcfeval ? "<li>Cleary, J. G., Braithwaite, R., Gaastra, K., Hilbush, B. S., Inglis, S., Irvine, S. A., Jackson, A., Littin, R., Rathod, M., Ware, D., Zook, J. M., Trigg, L., & Vega, F. M. D. L. (2015). Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines (p. 023754). bioRxiv. https://doi.org/10.1101/023754</li>" : "",
         "<li>Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352</li>",
         (!params.skip_smncopynumbercaller && params.analysis_type.equals("wgs")) ? "<li>Chen, X., Sanchis-Juan, A., French, C. E., Connell, A. J., Delon, I., Kingsbury, Z., Chawla, A., Halpern, A. L., Taft, R. J., Bentley, D. R., Butchbach, M. E. R., Raymond, F. L., & Eberle, M. A. (2020). Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genetics in Medicine, 22(5), 945–953. https://doi.org/10.1038/s41436-020-0754-0</li>" : "",
-        "<li>Li, H. (2011). Tabix: Fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics, 27(5), 718–719. https://doi.org/10.1093/bioinformatics/btq671</li>"
+        "<li>Li, H. (2011). Tabix: Fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics, 27(5), 718–719. https://doi.org/10.1093/bioinformatics/btq671</li>",
+        "<li>Quinlan, AR., Hall IM. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinfomatics, 26(6), 841-842. https://doi.org/10.1093/bioinformatics/btq033</li>"
     ]
 
     def concat_text = align_text +