diff --git a/CHANGELOG.md b/CHANGELOG.md
index bc90054c88..60d93f7426 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline.
 - [#1271](https://github.com/nf-core/sarek/pull/1271) - Back to dev
 
 ### Changed
diff --git a/conf/modules/prepare_genome.config b/conf/modules/prepare_genome.config
index 66eb2041d2..85367196c2 100644
--- a/conf/modules/prepare_genome.config
+++ b/conf/modules/prepare_genome.config
@@ -76,7 +76,7 @@ process {
     }
 
     withName: 'TABIX_DBSNP' {
-        ext.when         = { !params.dbsnp_tbi && params.dbsnp && ((params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('mutect2'))) }
+        ext.when         = { !params.dbsnp_tbi && params.dbsnp && ((params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope') || params.tools.split(',').contains('mutect2'))) }
         publishDir       = [
             enabled: (params.save_reference || params.build_only_index),
             mode: params.publish_dir_mode,
@@ -96,7 +96,7 @@ process {
     }
 
     withName: 'TABIX_KNOWN_INDELS' {
-        ext.when         = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper'))) ) }
+        ext.when         = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope'))) ) }
         publishDir       = [
             enabled: (params.save_reference || params.build_only_index),
             mode: params.publish_dir_mode,
@@ -106,7 +106,7 @@ process {
     }
 
     withName: 'TABIX_KNOWN_SNPS' {
-        ext.when         = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper'))) ) }
+        ext.when         = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') )) ) }
         publishDir       = [
             enabled: (params.save_reference || params.build_only_index),
             mode: params.publish_dir_mode,
diff --git a/conf/modules/sentieon_dnascope.config b/conf/modules/sentieon_dnascope.config
new file mode 100644
index 0000000000..fa431ae417
--- /dev/null
+++ b/conf/modules/sentieon_dnascope.config
@@ -0,0 +1,68 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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.
+----------------------------------------------------------------------------------------
+*/
+
+// SENTIEON DNASCOPE
+
+process {
+
+    withName: 'SENTIEON_DNASCOPE' {
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.dnascope" : "${meta.id}.dnascope.${intervals.simpleName}" }
+        ext.when         = { params.tools && params.tools.split(',').contains('sentieon_dnascope') }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/"},
+            pattern: "*{vcf.gz,vcf.gz.tbi}",
+            saveAs: { meta.num_intervals > 1 ? null : "sentieon_dnascope/${meta.id}/${it}" }
+        ]
+    }
+
+    withName: 'MERGE_SENTIEON_DNASCOPE_VCFS' {
+        ext.prefix       = { params.joint_germline ? "${meta.id}.dnascope.g" : "${meta.id}.dnascope.unfiltered" }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/sentieon_dnascope/${meta.id}/" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'MERGE_SENTIEON_DNASCOPE_GVCFS' {
+        ext.prefix       = { "${meta.id}.dnascope.g" }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/sentieon_dnascope/${meta.id}/" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    if (params.tools && params.tools.contains('sentieon_dnascope')) {
+        withName: '.*FILTERVARIANTTRANCHES' {
+            ext.prefix       = {"${meta.id}.dnascope"}
+            ext.args         = { "--info-key CNN_1D" }
+            publishDir       = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/sentieon_dnascope/${meta.id}/"},
+                pattern: "*{vcf.gz,vcf.gz.tbi}"
+            ]
+        }
+    }
+
+    withName: 'SENTIEON_DNAMODELAPPLY' {
+        ext.prefix       = {"${meta.id}.dnascope.filtered"}
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/sentieon_dnascope/${meta.id}/"},
+            pattern: "*{vcf.gz,vcf.gz.tbi}"
+        ]
+    }
+
+}
diff --git a/conf/modules/sentieon_dnascope_joint_germline.config b/conf/modules/sentieon_dnascope_joint_germline.config
new file mode 100644
index 0000000000..72dd6c3144
--- /dev/null
+++ b/conf/modules/sentieon_dnascope_joint_germline.config
@@ -0,0 +1,45 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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.
+----------------------------------------------------------------------------------------
+*/
+
+// SENTIEON DNASCOPE JOINT_GERMLINE
+
+process {
+
+    // TO-DO: duplicate!!
+    withName: 'SENTIEON_GVCFTYPER' {
+        ext.args         = { "--allow-old-rms-mapping-quality-annotation-data" }
+        ext.prefix       = { meta.intervals_name }
+        publishDir       = [
+            enabled: false
+        ]
+    }
+
+    if (params.tools && params.tools.contains('sentieon_dnascope') && params.joint_germline) {
+        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_SENTIEON:BCFTOOLS_SORT' {
+            ext.prefix       = { vcf.baseName - ".vcf" + ".sort" }
+            publishDir       = [
+                enabled: false
+            ]
+        }
+
+        withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_SENTIEON:MERGE_GENOTYPEGVCFS' {
+            ext.prefix       = "joint_germline"
+            publishDir       = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/sentieon_dnascope/joint_variant_calling/" },
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                pattern: "*{vcf.gz,vcf.gz.tbi}"
+            ]
+        }
+    }
+}
diff --git a/conf/modules/sentieon_joint_germline.config b/conf/modules/sentieon_haplotyper_joint_germline.config
similarity index 100%
rename from conf/modules/sentieon_joint_germline.config
rename to conf/modules/sentieon_haplotyper_joint_germline.config
diff --git a/docs/output.md b/docs/output.md
index b250ed2817..b03f4c11d0 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -37,8 +37,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
       - [GATK Germline Single Sample Variant Calling](#gatk-germline-single-sample-variant-calling)
       - [GATK Joint Germline Variant Calling](#gatk-joint-germline-variant-calling)
     - [GATK Mutect2](#gatk-mutect2)
+    - [Sentieon DNAscope](#sentieon-dnascope)
+      - [Sentieon DNAscope joint germline variant calling](#sentieon-dnascope-joint-germline-variant-calling)
     - [Sentieon Haplotyper](#sentieon-haplotyper)
-      - [Sentieon Joint Germline Variant Calling](#sentieon-joint-germline-variant-calling)
+      - [Sentieon Haplotyper joint germline variant calling](#sentieon-haplotyper-joint-germline-variant-calling)
     - [Strelka2](#strelka2)
   - [Structural Variants](#structural-variants)
     - [Manta](#manta)
@@ -442,6 +444,53 @@ Files created:
 
 </details>
 
+#### Sentieon DNAscope
+
+[Sentieon DNAscope](https://support.sentieon.com/appnotes/dnascope_ml/#dnascope-germline-variant-calling-with-a-machine-learning-model) is a variant-caller which aims at outperforming GATK's Haplotypecaller in terms of both speed and accuracy. DNAscope allows you to use a machine learning model to perform variant calling with higher accuracy by improving the candidate detection and filtering.
+
+<details markdown="1">
+<summary>Unfiltered VCF-files for normal samples</summary>
+
+**Output directory: `{outdir}/variantcalling/sentieon_dnascope/<sample>/`**
+
+- `<sample>.dnascope.unfiltered.vcf.gz` and `<sample>.dnascope.unfiltered.vcf.gz.tbi`
+  - VCF with tabix index
+
+</details>
+
+The output from Sentieon's DNAscope can be controlled through the option `--sentieon_dnascope_emit_mode` for Sarek, see [Basic usage of Sentieon functions](#basic-usage-of-sentieon-functions).
+
+Unless `dnascope_filter` is listed under `--skip_tools` in the nextflow command, Sentieon's [DNAModelApply](https://support.sentieon.com/manual/usages/general/#dnamodelapply-algorithm) is applied to the unfiltered VCF-files in order to obtain filtered VCF-files.
+
+<details markdown="1">
+<summary>Filtered VCF-files for normal samples</summary>
+
+**Output directory: `{outdir}/variantcalling/sentieon_dnascope/<sample>/`**
+
+- `<sample>.dnascope.filtered.vcf.gz` and `<sample>.dnascope.filtered.vcf.gz.tbi`
+  - VCF with tabix index
+
+</details>
+
+##### Sentieon DNAscope joint germline variant calling
+
+In Sentieon's package DNAscope, joint germline variant calling is done by first running Sentieon's Dnacope in emit-mode `gvcf` for each sample and then running Sentieon's [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) on the set of gVCF-files. See [Basic usage of Sentieon functions](#basic-usage-of-sentieon-functions) for information on how joint germline variant calling can be done in Sarek using Sentieon's DNAscope.
+
+<details markdown="1">
+<summary>Output files from joint germline variant calling</summary>
+
+**Output directory: `{outdir}/variantcalling/sentieon_dnascope/<sample>/`**
+
+- `<sample>.dnascope.g.vcf.gz` and `<sample>.dnascope.g.vcf.gz.tbi`
+  - VCF with tabix index
+
+**Output directory: `{outdir}/variantcalling/sentieon_dnascope/joint_variant_calling/`**
+
+- `joint_germline.vcf.gz` and `joint_germline.vcf.gz.tbi`
+  - VCF with tabix index
+
+</details>
+
 #### Sentieon Haplotyper
 
 [Sentieon Haplotyper](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm) is Sention's speedup version of GATK's Haplotypecaller (see above).
@@ -456,7 +505,7 @@ Files created:
 
 </details>
 
-The output from Sentieon's Haplotyper can be controlled through the option `--sentieon_haplotyper_emit_mode` for Sarek, see [Basic usage of Sentieon functions in Sarek](#basic-usage-of-sentieon-functions-in-sarek).
+The output from Sentieon's Haplotyper can be controlled through the option `--sentieon_haplotyper_emit_mode` for Sarek, see [Basic usage of Sentieon functions](#basic-usage-of-sentieon-functions).
 
 Unless `haplotyper_filter` is listed under `--skip_tools` in the nextflow command, GATK's CNNScoreVariants and FilterVariantTranches (see above) is applied to the unfiltered VCF-files in order to obtain filtered VCF-files.
 
@@ -470,16 +519,16 @@ Unless `haplotyper_filter` is listed under `--skip_tools` in the nextflow comman
 
 </details>
 
-##### Sentieon Joint Germline Variant Calling
+##### Sentieon Haplotyper joint germline variant calling
 
-In Sentieon's package DNAseq, joint germline variant calling is done by first running Sentieon's Haplotyper in emit-mode `gvcf` for each sample and then running Sentieon's [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) on the set of gVCF-files. See [Basic usage of Sentieon functions in Sarek](#basic-usage-of-sentieon-functions-in-sarek) for information on how joint germline variant calling can be done in Sarek using Sentieon's DNAseq. After joint genotyping, Sentieon's version of VQSR ([VarCal](https://support.sentieon.com/manual/usages/general/#varcal-algorithm) and [ApplyVarCal](https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm)) is applied for filtering to produce the final multisample callset with the desired balance of precision and sensitivity.
+In Sentieon's package DNAseq, joint germline variant calling is done by first running Sentieon's Haplotyper in emit-mode `gvcf` for each sample and then running Sentieon's [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) on the set of gVCF-files. See [Basic usage of Sentieon functions](#basic-usage-of-sentieon-functions) for information on how joint germline variant calling can be done in Sarek using Sentieon's DNAseq. After joint genotyping, Sentieon's version of VQSR ([VarCal](https://support.sentieon.com/manual/usages/general/#varcal-algorithm) and [ApplyVarCal](https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm)) is applied for filtering to produce the final multisample callset with the desired balance of precision and sensitivity.
 
 <details markdown="1">
 <summary>Output files from joint germline variant calling</summary>
 
 **Output directory: `{outdir}/variantcalling/sentieon_haplotyper/<sample>/`**
 
-- `<sample>.haplotypecaller.g.vcf.gz` and `<sample>.haplotypecaller.g.vcf.gz.tbi`
+- `<sample>.haplotyper.g.vcf.gz` and `<sample>.haplotyper.g.vcf.gz.tbi`
   - VCF with tabix index
 
 **Output directory: `{outdir}/variantcalling/sentieon_haplotyper/joint_variant_calling/`**
diff --git a/docs/usage.md b/docs/usage.md
index 0895fac23c..3b2767b302 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1083,7 +1083,9 @@ nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic>
 
 ### Available Sentieon functions
 
-Sarek contains the following Sentieon functions [bwa mem](https://support.sentieon.com/manual/usages/general/#bwa-mem-syntax), [LocusCollector](https://support.sentieon.com/manual/usages/general/#locuscollector-algorithm) + [Dedup](https://support.sentieon.com/manual/usages/general/#dedup-algorithm), [Haplotyper](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm), [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) and [VarCal](https://support.sentieon.com/manual/usages/general/#varcal-algorithm) + [ApplyVarCal](https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm), so the basic processing of alignment of fastq-files to VCF-files can be done using speedup Sentieon functions.
+Sarek contains the following Sentieon functions from [DnaSeq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/) : [bwa mem](https://support.sentieon.com/manual/usages/general/#bwa-mem-syntax), [LocusCollector](https://support.sentieon.com/manual/usages/general/#locuscollector-algorithm) + [Dedup](https://support.sentieon.com/manual/usages/general/#dedup-algorithm), [Haplotyper](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm), [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) and [VarCal](https://support.sentieon.com/manual/usages/general/#varcal-algorithm) + [ApplyVarCal](https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm), so the basic processing of alignment of fastq-files to VCF-files can be done using speedup Sentieon functions.
+
+Sarek also contains the Sentieon functions [DnaScope](https://support.sentieon.com/manual/usages/general/?highlight=dnamodelapply#dnascope-algorithm) and [DNAModelApply](https://support.sentieon.com/manual/usages/general/?highlight=dnamodelapply#dnamodelapply-algorithm).
 
 ### Basic usage of Sentieon functions
 
@@ -1091,9 +1093,11 @@ To use Sentieon's aligner `bwa mem`, set the aligner option `sentieon-bwamem`. (
 
 To use Sentieon's function `Dedup`, specify `sentieon_dedup` as one of the tools. (This can, for example, be done by adding `--tools sentieon_dedup` to the nextflow run command.)
 
-To use Sentieon's function `Haplotyper`, specify `sentieon_haplotyper` as one of the tools. This can, for example, be done by adding `--tools sentieon_haplotyper` to the nextflow run command. In order to skip the GATK-based variant-filter, one may add `--skip_tools haplotyper_filter` to the nextflow run command. Sarek also provides the option `sentieon_haplotyper_emit_mode` which can be used to set the [emit-mode](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm) of Sentieon's haplotyper. Sentieon's haplotyper can output both a vcf-file and a gvcf-file in the same run; this is achieved by setting `sentieon_haplotyper_emit_mode` to `<vcf_emit_mode>,gvcf`, where `<vcf_emit_mode>` is `variant`, `confident` or `all`.
+To use Sentieon's function `DNAscope`, specify `sentieon_dnascope` as one of the tools. This can, for example, be done by adding `--tools sentieon_dnascope` to the nextflow run command. In order to skip Sentieon's variant-filter `DNAModelApply`, one may add `--skip_tools dnascope_filter` to the nextflow run command. Sarek also provides the option `sentieon_dnascope_emit_mode` which can be used to set the [emit-mode](https://support.sentieon.com/manual/usages/general/#dnascope-algorithm) of Sentieon's dnascope. Sentieon's dnascope can output both a vcf-file and a gvcf-file in the same run; this is achieved by setting `sentieon_dnascope_emit_mode` to `<vcf_emit_mode>,gvcf`, where `<vcf_emit_mode>` is `variant`, `confident` or `all`.
+
+Sentieon's function `Haplotyper` is used in much the same way as `DNAscope`. To use Sentieon's function `Haplotyper`, specify `sentieon_haplotyper` as one of the tools. This can, for example, be done by adding `--tools sentieon_haplotyper` to the nextflow run command. In order to skip the GATK-based variant-filter, one may add `--skip_tools haplotyper_filter` to the nextflow run command. Sarek also provides the option `sentieon_haplotyper_emit_mode` which can be used to set the [emit-mode](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm) of Sentieon's haplotyper. Sentieon's haplotyper can output both a vcf-file and a gvcf-file in the same run; this is achieved by setting `sentieon_haplotyper_emit_mode` to `<vcf_emit_mode>,gvcf`, where `<vcf_emit_mode>` is `variant`, `confident` or `all`.
 
-To use Sentieon's function `GVCFtyper` along with Sention's version of VQSR (`VarCal` and `ApplyVarCal`) for joint-germline genotyping, specify `sentieon_haplotyper` as one of the tools, set the option `sentieon_haplotyper_emit_mode` to `gvcf`, and add the option `joint_germline`. This can, for example, be done by adding `--tools sentieon_haplotyper --joint_germline --sentieon_haplotyper_emit_mode gvcf` to the nextflow run command.
+To use Sentieon's function `GVCFtyper` along with Sention's version of VQSR (`VarCal` and `ApplyVarCal`) for joint-germline genotyping, specify `sentieon_haplotyper` as one of the tools, set the option `sentieon_haplotyper_emit_mode` to `gvcf`, and add the option `joint_germline`. This can, for example, be done by adding `--tools sentieon_haplotyper --joint_germline --sentieon_haplotyper_emit_mode gvcf` to the nextflow run command. If `sentieon_dnascope` is chosen instead of `sentieon_haplotyper`, then Sention's version of VQSR is skipped, as recommended by Sentieon.
 
 ### Joint germline variant calling
 
diff --git a/modules.json b/modules.json
index 84b30a76dc..06ff0b6dab 100644
--- a/modules.json
+++ b/modules.json
@@ -388,6 +388,16 @@
                         "git_sha": "915a0b16ba3e40ef59e7b44843b3118e17a9c906",
                         "installed_by": ["modules"]
                     },
+                    "sentieon/dnamodelapply": {
+                        "branch": "master",
+                        "git_sha": "43ef68091a1188fd8dc4c03f9341b556803c7514",
+                        "installed_by": ["modules"]
+                    },
+                    "sentieon/dnascope": {
+                        "branch": "master",
+                        "git_sha": "4fb6fdc8046ec09cd30f92a2a252e9a0ba4a6309",
+                        "installed_by": ["modules"]
+                    },
                     "sentieon/gvcftyper": {
                         "branch": "master",
                         "git_sha": "6c9c11ee96796e53a01b4719286acce6af14bc3a",
diff --git a/modules/nf-core/sentieon/dnamodelapply/main.nf b/modules/nf-core/sentieon/dnamodelapply/main.nf
new file mode 100644
index 0000000000..3fe9a28f19
--- /dev/null
+++ b/modules/nf-core/sentieon/dnamodelapply/main.nf
@@ -0,0 +1,81 @@
+process SENTIEON_DNAMODELAPPLY {
+    tag "$meta.id"
+    label 'process_high'
+    label 'sentieon'
+
+    secret 'SENTIEON_LICENSE_BASE64'
+
+    container 'nf-core/sentieon:202112.06'
+
+    input:
+    tuple val(meta), path(vcf), path(idx)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(ml_model)
+
+    output:
+    tuple val(meta), path("*.vcf.gz")    , emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi"), emit: index
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args      = task.ext.args   ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
+    def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
+
+    """
+    if [ "\${#SENTIEON_LICENSE_BASE64}" -lt "1500" ]; then  # If the string SENTIEON_LICENSE_BASE64 is short, then it is an encrypted url.
+        export SENTIEON_LICENSE=\$(echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d)
+    else  # Localhost license file
+        # The license file is stored as a nextflow variable like, for instance, this:
+        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
+        export SENTIEON_LICENSE=\$(mktemp)
+        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
+    fi
+
+    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
+        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
+        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
+        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
+        echo "Decoded and exported Sentieon test-license system environment variables"
+    fi
+
+    sentieon driver \\
+        -t $task.cpus \\
+        -r $fasta \\
+        $args \\
+        --algo DNAModelApply \\
+        --model $ml_model \\
+        -v $vcf \\
+        ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    """
+    touch ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/sentieon/dnamodelapply/meta.yml b/modules/nf-core/sentieon/dnamodelapply/meta.yml
new file mode 100644
index 0000000000..ec429bea21
--- /dev/null
+++ b/modules/nf-core/sentieon/dnamodelapply/meta.yml
@@ -0,0 +1,78 @@
+name: "sentieon_dnamodelapply"
+description: modifies the input VCF file by adding the MLrejected FILTER to the variants
+keywords:
+  - dnamodelapply
+  - vcf
+  - filter
+  - sentieon
+tools:
+  - sentieon:
+      description: |
+        Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.
+        Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
+      homepage: https://www.sentieon.com/
+      documentation: https://www.sentieon.com/
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'test' ]`
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'test' ]`
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. `[ id:'test' ]`
+  - vcf:
+      type: file
+      description: INPUT VCF file
+      pattern: "*.{vcf,vcf.gz}"
+  - idx:
+      type: file
+      description: Index of the input VCF file
+      pattern: "*.{tbi}"
+  - fasta:
+      type: file
+      description: Genome fasta file
+      pattern: "*.{fa,fasta}"
+  - fai:
+      type: file
+      description: Index of the genome fasta file
+      pattern: "*.fai"
+  - ml_model:
+      type: file
+      description: machine learning model file
+      pattern: "*.model"
+
+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: INPUT VCF file
+      pattern: "*.{vcf,vcf.gz}"
+  - index:
+      type: file
+      description: Index of the input VCF file
+      pattern: "*.{tbi}"
+
+authors:
+  - "@ramprasadn"
diff --git a/modules/nf-core/sentieon/dnascope/main.nf b/modules/nf-core/sentieon/dnascope/main.nf
new file mode 100644
index 0000000000..6be42a1728
--- /dev/null
+++ b/modules/nf-core/sentieon/dnascope/main.nf
@@ -0,0 +1,100 @@
+process SENTIEON_DNASCOPE {
+    tag "$meta.id"
+    label 'process_high'
+    label 'sentieon'
+
+    secret 'SENTIEON_LICENSE_BASE64'
+
+    container 'nf-core/sentieon:202112.06'
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(intervals)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dbsnp)
+    tuple val(meta5), path(dbsnp_tbi)
+    tuple val(meta6), path(ml_model)
+    val(pcr_indel_model)
+    val(emit_vcf)
+    val(emit_gvcf)
+
+    output:
+    tuple val(meta), path("*.unfiltered.vcf.gz")    , optional:true, emit: vcf   // added the substring ".unfiltered" in the filename of the vcf-files since without that the g.vcf.gz-files were ending up in the vcf-channel
+    tuple val(meta), path("*.unfiltered.vcf.gz.tbi"), optional:true, emit: vcf_tbi
+    tuple val(meta), path("*.g.vcf.gz")             , optional:true, emit: gvcf   // these output-files have to have the extension ".vcf.gz", otherwise the subsequent GATK-MergeVCFs will fail.
+    tuple val(meta), path("*.g.vcf.gz.tbi")         , optional:true, emit: gvcf_tbi
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args                      = task.ext.args                      ?: ''  // options for the driver
+    def args2                     = task.ext.args2                     ?: ''  // options for the vcf generation
+    def args3                     = task.ext.args3                     ?: ''  // options for the gvcf generation
+    def interval                  = intervals                          ? "--interval ${intervals}"               : ''
+    def dbsnp_cmd                 = dbsnp                              ? "-d ${dbsnp}"                           : ''
+    def model_cmd                 = ml_model                           ? " --model ${ml_model}"                  : ''
+    def pcr_indel_model_cmd       = pcr_indel_model                    ? " --pcr_indel_model ${pcr_indel_model}" : ''
+    def prefix                    = task.ext.prefix                    ?: "${meta.id}"
+    def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
+    def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
+    def vcf_cmd                   = ""
+    def gvcf_cmd                  = ""
+    def base_cmd                  = '--algo DNAscope ' + dbsnp_cmd + ' '
+
+    if (emit_vcf) {  // emit_vcf can be the empty string, 'variant', 'confident' or 'all' but NOT 'gvcf'
+        vcf_cmd = base_cmd + args2 + ' ' + model_cmd + pcr_indel_model_cmd + ' --emit_mode ' + emit_vcf + ' ' + prefix + '.unfiltered.vcf.gz'
+    }
+
+    if (emit_gvcf) { // emit_gvcf can be either true or false
+        gvcf_cmd = base_cmd + args3 + ' ' + model_cmd + pcr_indel_model_cmd + ' --emit_mode gvcf ' + prefix + '.g.vcf.gz'
+    }
+
+    """
+    if [ "\${#SENTIEON_LICENSE_BASE64}" -lt "1500" ]; then  # If the string SENTIEON_LICENSE_BASE64 is short, then it is an encrypted url.
+        export SENTIEON_LICENSE=\$(echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d)
+    else  # Localhost license file
+        # The license file is stored as a nextflow variable like, for instance, this:
+        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
+        export SENTIEON_LICENSE=\$(mktemp)
+        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
+    fi
+
+    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
+        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
+        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
+        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
+        echo "Decoded and exported Sentieon test-license system environment variables"
+    fi
+
+    sentieon driver $args -r $fasta -t $task.cpus -i $bam $interval $vcf_cmd $gvcf_cmd
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    """
+    touch ${prefix}.unfiltered.vcf.gz
+    touch ${prefix}.unfiltered.vcf.gz.tbi
+    touch ${prefix}.g.vcf.gz
+    touch ${prefix}.g.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/sentieon/dnascope/meta.yml b/modules/nf-core/sentieon/dnascope/meta.yml
new file mode 100644
index 0000000000..34e0b97b4c
--- /dev/null
+++ b/modules/nf-core/sentieon/dnascope/meta.yml
@@ -0,0 +1,119 @@
+name: sentieon_dnascope
+description: DNAscope algorithm performs an improved version of Haplotype variant calling.
+keywords:
+  - dnascope
+  - sentieon
+  - variant_calling
+tools:
+  - sentieon:
+      description: |
+        Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.
+        Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
+      homepage: https://www.sentieon.com/
+      documentation: https://www.sentieon.com/
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information.
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file.
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: BAI file
+      pattern: "*.bai"
+  - intervals:
+      type: file
+      description: bed or interval_list file containing interval in the reference that will be used in the analysis
+      pattern: "*.{bed,interval_list}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing meta information for fasta.
+  - fasta:
+      type: file
+      description: Genome fasta file
+      pattern: "*.{fa,fasta}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing meta information for fasta index.
+  - fai:
+      type: file
+      description: Index of the genome fasta file
+      pattern: "*.fai"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing meta information for dbsnp.
+  - dbsnp:
+      type: file
+      description: Single Nucleotide Polymorphism database (dbSNP) file
+      pattern: "*.vcf.gz"
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing meta information for dbsnp_tbi.
+  - dbsnp_tbi:
+      type: file
+      description: Index of the Single Nucleotide Polymorphism database (dbSNP) file
+      pattern: "*.vcf.gz.tbi"
+  - meta6:
+      type: map
+      description: |
+        Groovy Map containing meta information for machine learning model for Dnascope.
+  - ml_model:
+      type: file
+      description: machine learning model file
+      pattern: "*.model"
+  - ml_model:
+      type: file
+      description: machine learning model file
+      pattern: "*.model"
+  - pcr_indel_model:
+      type: string
+      description: |
+        Controls the option pcr_indel_model for Dnascope.
+        The possible options are "NONE" (used for PCR free samples), and "HOSTILE", "AGGRESSIVE" and "CONSERVATIVE".
+        See Sentieons documentation for further explanation.
+  - emit_vcf:
+      type: string
+      description: |
+        Controls the vcf output from Dnascope.
+        Possible options are "all", "confident" and "variant".
+        See Sentieons documentation for further explanation.
+  - emit_gvcf:
+      type: boolean
+      description: If true, the haplotyper will output a gvcf
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information.
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: Compressed VCF file
+      pattern: "*.unfiltered.vcf.gz"
+  - vcf_tbi:
+      type: file
+      description: Index of VCF file
+      pattern: "*.unfiltered.vcf.gz.tbi"
+  - gvcf:
+      type: file
+      description: Compressed GVCF file
+      pattern: "*.g.vcf.gz"
+  - gvcf_tbi:
+      type: file
+      description: Index of GVCF file
+      pattern: "*.g.vcf.gz.tbi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@ramprasadn"
diff --git a/nextflow.config b/nextflow.config
index ccf3f5068c..56cab933a6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -51,26 +51,29 @@ params {
     seq_platform       = 'ILLUMINA' // Default platform written in read group PL field by aligner
 
     // Variant Calling
-    only_paired_variant_calling   = false // if true, skips germline variant calling for normal-paired samples
-    ascat_ploidy                  = null  // default value for ASCAT
-    ascat_min_base_qual           = 20    // default value for ASCAT
-    ascat_min_counts              = 10    // default value for ASCAT
-    ascat_min_map_qual            = 35    // default value for ASCAT
-    ascat_purity                  = null  // default value for ASCAT
-    cf_ploidy                     = "2"   // default value for Control-FREEC
-    cf_coeff                      = 0.05  // default value for Control-FREEC
-    cf_contamination              = 0     // default value for Control-FREEC
-    cf_contamination_adjustment   = false // by default we are not using this in Control-FREEC
-    cf_mincov                     = 0     // ControlFreec default values
-    cf_minqual                    = 0     // ControlFreec default values
-    cf_window                     = null  // by default we are not using this in Control-FREEC
-    cnvkit_reference              = null  // by default the reference is build from the fasta file
-    concatenate_vcfs              = false // by default we don't concatenate the germline-vcf-files
-    ignore_soft_clipped_bases     = false // no --dont-use-soft-clipped-bases for GATK Mutect2
-    wes                           = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers
-    joint_germline                = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected
-    joint_mutect2                = false // if true, enables patient-wise multi-sample somatic variant calling
-    sentieon_haplotyper_emit_mode = "variant" // default value for Sentieon haplotyper
+    ascat_ploidy                      = null  // default value for ASCAT
+    ascat_min_base_qual               = 20    // default value for ASCAT
+    ascat_min_counts                  = 10    // default value for ASCAT
+    ascat_min_map_qual                = 35    // default value for ASCAT
+    ascat_purity                      = null  // default value for ASCAT
+    cf_ploidy                         = "2"   // default value for Control-FREEC
+    cf_coeff                          = 0.05  // default value for Control-FREEC
+    cf_contamination                  = 0     // default value for Control-FREEC
+    cf_contamination_adjustment       = false // by default we are not using this in Control-FREEC
+    cf_mincov                         = 0     // ControlFreec default values
+    cf_minqual                        = 0     // ControlFreec default values
+    cf_window                         = null  // by default we are not using this in Control-FREEC
+    cnvkit_reference                  = null  // by default the reference is build from the fasta file
+    concatenate_vcfs                  = false // by default we don't concatenate the germline-vcf-files
+    ignore_soft_clipped_bases         = false // no --dont-use-soft-clipped-bases for GATK Mutect2
+    joint_germline                    = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected
+    joint_mutect2                     = false // if true, enables patient-wise multi-sample somatic variant calling
+    only_paired_variant_calling       = false // if true, skips germline variant calling for normal-paired sample
+    sentieon_dnascope_emit_mode       = "variant" // default value for Sentieon dnascope
+    sentieon_dnascope_model           = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model"
+    sentieon_dnascope_pcr_indel_model = "CONSERVATIVE"
+    sentieon_haplotyper_emit_mode     = "variant" // default value for Sentieon haplotyper
+    wes                               = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers
 
     // Annotation
     dbnsfp                    = null // No dbnsfp processed file
@@ -377,8 +380,10 @@ includeConfig 'conf/modules/manta.config'
 includeConfig 'conf/modules/mpileup.config'
 includeConfig 'conf/modules/msisensorpro.config'
 includeConfig 'conf/modules/mutect2.config'
+includeConfig 'conf/modules/sentieon_dnascope.config'
+includeConfig 'conf/modules/sentieon_dnascope_joint_germline.config'
 includeConfig 'conf/modules/sentieon_haplotyper.config'
-includeConfig 'conf/modules/sentieon_joint_germline.config'
+includeConfig 'conf/modules/sentieon_haplotyper_joint_germline.config'
 includeConfig 'conf/modules/strelka.config'
 includeConfig 'conf/modules/tiddit.config'
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 51850b6fa9..68c6b77146 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -100,14 +100,14 @@
                     "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, Strelka2\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).\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|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
+                    "pattern": "^((ascat|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
                 },
                 "skip_tools": {
                     "type": "string",
                     "fa_icon": "fas fa-forward",
                     "description": "Disable specified tools.",
                     "help_text": "Multiple tools can be specified, separated by commas.\n\n> **NB** `--skip_tools baserecalibrator_report` is actually just not saving the reports.\n> **NB** `--skip_tools markduplicates_report` does not skip `MarkDuplicates` but prevent the collection of duplicate metrics that slows down performance.",
-                    "pattern": "^((baserecalibrator|baserecalibrator_report|bcftools|documentation|fastqc|haplotypecaller_filter|haplotyper_filter|markduplicates|markduplicates_report|mosdepth|multiqc|samtools|vcftools|versions)?,?)*(?<!,)$"
+                    "pattern": "^((baserecalibrator|baserecalibrator_report|bcftools|dnascope_filter|documentation|fastqc|haplotypecaller_filter|haplotyper_filter|markduplicates|markduplicates_report|mosdepth|multiqc|samtools|vcftools|versions)?,?)*(?<!,)$"
                 }
             },
             "fa_icon": "fas fa-user-cog"
@@ -391,6 +391,28 @@
                     "description": "Option for selecting output and emit-mode of Sentieon's Haplotyper.",
                     "help_text": "The option `--sentieon_haplotyper_emit_mode` can be set to the same string values as the Haplotyper's `--emit_mode`. To output both a vcf and a gvcf, specify both a vcf-option (currently, `all`, `confident` and `variant`) and `gvcf`. For example, to obtain a vcf and gvcf one could set `--sentieon_haplotyper_emit_mode` to `variant, gvcf`.",
                     "pattern": "^(all|confident|gvcf|variant|gvcf,all|gvcf,confident|gvcf,variant|all,gvcf|confident,gvcf|variant,gvcf)(?<!,)$"
+                },
+                "sentieon_dnascope_emit_mode": {
+                    "type": "string",
+                    "default": "variant",
+                    "fa_icon": "fas fa-toolbox",
+                    "description": "Option for selecting output and emit-mode of Sentieon's Dnascope.",
+                    "help_text": "The option `--sentieon_dnascope_emit_mode` can be set to the same string values as the Dnascope's `--emit_mode`. To output both a vcf and a gvcf, specify both a vcf-option (currently, `all`, `confident` and `variant`) and `gvcf`. For example, to obtain a vcf and gvcf one could set `--sentieon_dnascope_emit_mode` to `variant, gvcf`.",
+                    "pattern": "^(all|confident|gvcf|variant|gvcf,all|gvcf,confident|gvcf,variant|all,gvcf|confident,gvcf|variant,gvcf)(?<!,)$"
+                },
+                "sentieon_dnascope_pcr_indel_model": {
+                    "type": "string",
+                    "default": "CONSERVATIVE",
+                    "fa_icon": "fas fa-bacon",
+                    "description": "Option for selecting the PCR indel model used by Sentieon Dnascope.",
+                    "help_text": "PCR indel model used to weed out false positive indels more or less aggressively. The possible MODELs are: NONE (used for PCR free samples), and HOSTILE, AGGRESSIVE and CONSERVATIVE, in order of decreasing aggressiveness. The default value is CONSERVATIVE.",
+                    "pattern": "^(NONE|HOSTILE|AGGRESSIVE|CONSERVATIVE)(?<!,)$"
+                },
+                "sentieon_dnascope_model": {
+                    "type": "string",
+                    "fa_icon": "fas fa-database",
+                    "description": "Machine learning model for Sentieon Dnascope.",
+                    "help_text": " It is recommended to use DNAscope with a machine learning model to perform variant calling with higher accuracy by improving the candidate detection and filtering. Sentieon can provide you with a model trained using a subset of the data from the GiAB truth-set found in https://github.com/genome-in-a-bottle. In addition, Sentieon can assist you in the creation of models using your own data, which will calibrate the specifics of your sequencing and bio-informatics processing."
                 }
             }
         },
diff --git a/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf b/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf
index da8b0e60be..3f19b33d52 100644
--- a/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf
+++ b/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf
@@ -27,6 +27,7 @@ workflow BAM_JOINT_CALLING_GERMLINE_SENTIEON {
     resource_snps_vcf
     resource_snps_tbi
     known_snps_vqsr
+    variant_caller
 
     main:
     versions = Channel.empty()
@@ -39,96 +40,107 @@ workflow BAM_JOINT_CALLING_GERMLINE_SENTIEON {
 
     BCFTOOLS_SORT(SENTIEON_GVCFTYPER.out.vcf_gz)
 
-    gvcf_to_merge = BCFTOOLS_SORT.out.vcf.map{ meta, vcf -> [ meta.subMap('num_intervals') + [ id:'joint_variant_calling', patient:'all_samples', variantcaller:'sentieon_haplotyper' ], vcf ]}.groupTuple()
+    gvcf_to_merge = BCFTOOLS_SORT.out.vcf.map{ meta, vcf -> [ meta.subMap('num_intervals') + [ id:'joint_variant_calling', patient:'all_samples', variantcaller:variant_caller ], vcf ]}.groupTuple()
 
     // Merge scatter/gather vcfs & index
     // Rework meta for variantscalled.csv and annotation tools
     MERGE_GENOTYPEGVCFS(gvcf_to_merge, dict)
 
-    vqsr_input = MERGE_GENOTYPEGVCFS.out.vcf.join(MERGE_GENOTYPEGVCFS.out.tbi, failOnDuplicate: true)
-    indels_resource_label = known_indels_vqsr.mix(dbsnp_vqsr).collect()
-    snps_resource_label = known_snps_vqsr.mix(dbsnp_vqsr).collect()
-
-    // Recalibrate INDELs and SNPs separately
-    SENTIEON_VARCAL_INDEL(
-        vqsr_input,
-        resource_indels_vcf,
-        resource_indels_tbi,
-        indels_resource_label,
-        fasta,
-        fai)
-
-    SENTIEON_VARCAL_SNP(
-        vqsr_input,
-        resource_snps_vcf,
-        resource_snps_tbi,
-        snps_resource_label,
-        fasta,
-        fai)
-
-    //Prepare SNPs and INDELs for Sentieon's applyvarcal
-    // Step 1. : applyvarcal to SNPs
-    // Step 2. : Use SENTIEON_APPLYVARCAL_SNP output and run ApplyVQSR_INDEL. This avoids duplicate entries in the vcf as described here: https://hpc.nih.gov/training/gatk_tutorial/vqsr.html
-
-    // Join results of variant recalibration into a single channel tuple
-    // Rework meta for variantscalled.csv and annotation tools
-    vqsr_input_snp = vqsr_input.join(SENTIEON_VARCAL_SNP.out.recal, failOnDuplicate: true)
-        .join(SENTIEON_VARCAL_SNP.out.idx, failOnDuplicate: true)
-        .join(SENTIEON_VARCAL_SNP.out.tranches, failOnDuplicate: true)
-        .map{ meta, vcf, tbi, recal, index, tranche -> [ meta + [ id:'recalibrated_joint_variant_calling' ], vcf, tbi, recal, index, tranche ] }
-
-    SENTIEON_APPLYVARCAL_SNP(
-        vqsr_input_snp,
-        fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] },
-        fai.map{ fai -> [ [ id:fai.baseName ], fai ] })
-
-    // Join results of SENTIEON_APPLYVARCAL_SNP and use as input for SENTIEON_APPLYVARCAL_INDEL to avoid duplicate entries in the result
-    // Rework meta for variantscalled.csv and annotation tools
-    vqsr_input_indel = SENTIEON_APPLYVARCAL_SNP.out.vcf.join(SENTIEON_APPLYVARCAL_SNP.out.tbi).map{ meta, vcf, tbi -> [ meta + [ id:'joint_variant_calling' ], vcf, tbi ]}
-        .join(SENTIEON_VARCAL_INDEL.out.recal, failOnDuplicate: true)
-        .join(SENTIEON_VARCAL_INDEL.out.idx, failOnDuplicate: true)
-        .join(SENTIEON_VARCAL_INDEL.out.tranches, failOnDuplicate: true)
-        .map{ meta, vcf, tbi, recal, index, tranche -> [ meta + [ id:'recalibrated_joint_variant_calling' ], vcf, tbi, recal, index, tranche ] }
-
-    SENTIEON_APPLYVARCAL_INDEL(
-        vqsr_input_indel,
-        fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] },
-        fai.map{ fai -> [ [ id:fai.baseName ], fai ] })
-
-    // The following is an ugly monster to achieve the following:
-    // When MERGE_GENOTYPEGVCFS and SENTIEON_APPLYVARCAL are run, then use output from SENTIEON_APPLYVARCAL
-    // When MERGE_GENOTYPEGVCFS and NOT SENTIEON_APPLYVARCAL, then use the output from MERGE_GENOTYPEGVCFS
-
-    merge_vcf_for_join = MERGE_GENOTYPEGVCFS.out.vcf.map{meta, vcf -> [[id: 'joint_variant_calling'] , vcf]}
-    merge_tbi_for_join = MERGE_GENOTYPEGVCFS.out.tbi.map{meta, tbi -> [[id: 'joint_variant_calling'] , tbi]}
-
-    // Remap for both to have the same key, if ApplyBQSR is not run, the channel is empty --> populate with empty elements
-    vqsr_vcf_for_join = SENTIEON_APPLYVARCAL_INDEL.out.vcf.ifEmpty([[:], []]).map{meta, vcf -> [[id: 'joint_variant_calling'] , vcf]}
-    vqsr_tbi_for_join = SENTIEON_APPLYVARCAL_INDEL.out.tbi.ifEmpty([[:], []]).map{meta, tbi -> [[id: 'joint_variant_calling'] , tbi]}
-
-    // Join on metamap
-    // If both --> meta, vcf_merged, vcf_bqsr
-    // If not VQSR --> meta, vcf_merged, []
-    // if the second is empty, use the first
-    genotype_vcf = merge_vcf_for_join.join(vqsr_vcf_for_join, remainder: true).map{
-        meta, joint_vcf, recal_vcf ->
-
-        vcf_out = recal_vcf ?: joint_vcf
-
-        [[id:"joint_variant_calling", patient:"all_samples", variantcaller:"sentieon_haplotyper"], vcf_out]
-    }
-
-    genotype_index = merge_tbi_for_join.join(vqsr_tbi_for_join, remainder: true).map{
-        meta, joint_tbi, recal_tbi ->
-
-        tbi_out = recal_tbi ?: joint_tbi
-        [[id:"joint_variant_calling", patient:"all_samples", variantcaller:"sentieon_haplotyper"], tbi_out]
+    merged_vcf = MERGE_GENOTYPEGVCFS.out.vcf.map{meta, vcf -> [[id: 'joint_variant_calling'] , vcf]}
+    merged_tbi = MERGE_GENOTYPEGVCFS.out.tbi.map{meta, tbi -> [[id: 'joint_variant_calling'] , tbi]}
+
+    if (variant_caller == 'sentieon_dnascope') {
+        // As advised by Don Freed (Sentieon), VQSR is skipped for DnaScope
+        genotype_vcf   = merged_vcf.map{
+            meta, vcf -> [ meta + [ patient:"all_samples", variantcaller:'sentieon_dnascope'], vcf ]
+        }
+        genotype_index = merged_tbi.map{
+            meta, tbi -> [ meta + [ patient:"all_samples", variantcaller:'sentieon_dnascope'], tbi ]
+        }
+    } else {
+        vqsr_input = MERGE_GENOTYPEGVCFS.out.vcf.join(MERGE_GENOTYPEGVCFS.out.tbi, failOnDuplicate: true)
+        indels_resource_label = known_indels_vqsr.mix(dbsnp_vqsr).collect()
+        snps_resource_label = known_snps_vqsr.mix(dbsnp_vqsr).collect()
+
+        // Recalibrate INDELs and SNPs separately
+        SENTIEON_VARCAL_INDEL(
+            vqsr_input,
+            resource_indels_vcf,
+            resource_indels_tbi,
+            indels_resource_label,
+            fasta,
+            fai)
+
+        SENTIEON_VARCAL_SNP(
+            vqsr_input,
+            resource_snps_vcf,
+            resource_snps_tbi,
+            snps_resource_label,
+            fasta,
+            fai)
+
+        //Prepare SNPs and INDELs for Sentieon's applyvarcal
+        // Step 1. : applyvarcal to SNPs
+        // Step 2. : Use SENTIEON_APPLYVARCAL_SNP output and run ApplyVQSR_INDEL. This avoids duplicate entries in the vcf as described here: https://hpc.nih.gov/training/gatk_tutorial/vqsr.html
+
+        // Join results of variant recalibration into a single channel tuple
+        // Rework meta for variantscalled.csv and annotation tools
+        vqsr_input_snp = vqsr_input.join(SENTIEON_VARCAL_SNP.out.recal, failOnDuplicate: true)
+            .join(SENTIEON_VARCAL_SNP.out.idx, failOnDuplicate: true)
+            .join(SENTIEON_VARCAL_SNP.out.tranches, failOnDuplicate: true)
+            .map{ meta, vcf, tbi, recal, index, tranche -> [ meta + [ id:'recalibrated_joint_variant_calling' ], vcf, tbi, recal, index, tranche ] }
+
+        SENTIEON_APPLYVARCAL_SNP(
+            vqsr_input_snp,
+            fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] },
+            fai.map{ fai -> [ [ id:fai.baseName ], fai ] })
+
+        // Join results of SENTIEON_APPLYVARCAL_SNP and use as input for SENTIEON_APPLYVARCAL_INDEL to avoid duplicate entries in the result
+        // Rework meta for variantscalled.csv and annotation tools
+        vqsr_input_indel = SENTIEON_APPLYVARCAL_SNP.out.vcf.join(SENTIEON_APPLYVARCAL_SNP.out.tbi).map{ meta, vcf, tbi -> [ meta + [ id:'joint_variant_calling' ], vcf, tbi ]}
+            .join(SENTIEON_VARCAL_INDEL.out.recal, failOnDuplicate: true)
+            .join(SENTIEON_VARCAL_INDEL.out.idx, failOnDuplicate: true)
+            .join(SENTIEON_VARCAL_INDEL.out.tranches, failOnDuplicate: true)
+            .map{ meta, vcf, tbi, recal, index, tranche -> [ meta + [ id:'recalibrated_joint_variant_calling' ], vcf, tbi, recal, index, tranche ] }
+
+        SENTIEON_APPLYVARCAL_INDEL(
+            vqsr_input_indel,
+            fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] },
+            fai.map{ fai -> [ [ id:fai.baseName ], fai ] })
+
+        // The following is an ugly monster to achieve the following:
+        // When MERGE_GENOTYPEGVCFS and SENTIEON_APPLYVARCAL are run, then use output from SENTIEON_APPLYVARCAL
+        // When MERGE_GENOTYPEGVCFS and NOT SENTIEON_APPLYVARCAL, then use the output from MERGE_GENOTYPEGVCFS
+
+        // Remap for both to have the same key, if ApplyBQSR is not run, the channel is empty --> populate with empty elements
+        vqsr_vcf_for_join = SENTIEON_APPLYVARCAL_INDEL.out.vcf.ifEmpty([[:], []]).map{meta, vcf -> [[id: 'joint_variant_calling'] , vcf]}
+        vqsr_tbi_for_join = SENTIEON_APPLYVARCAL_INDEL.out.tbi.ifEmpty([[:], []]).map{meta, tbi -> [[id: 'joint_variant_calling'] , tbi]}
+
+        // Join on metamap
+        // If both --> meta, vcf_merged, vcf_bqsr
+        // If not VQSR --> meta, vcf_merged, []
+        // if the second is empty, use the first
+        genotype_vcf = merged_vcf.join(vqsr_vcf_for_join, remainder: true).map{
+            meta, joint_vcf, recal_vcf ->
+
+            vcf_out = recal_vcf ?: joint_vcf
+
+            [[id:"joint_variant_calling", patient:"all_samples", variantcaller:"sentieon_haplotyper"], vcf_out]
+        }
+
+        genotype_index = merged_tbi.join(vqsr_tbi_for_join, remainder: true).map{
+            meta, joint_tbi, recal_tbi ->
+
+            tbi_out = recal_tbi ?: joint_tbi
+            [[id:"joint_variant_calling", patient:"all_samples", variantcaller:"sentieon_haplotyper"], tbi_out]
+        }
+
+        versions = versions.mix(SENTIEON_VARCAL_SNP.out.versions)
+        versions = versions.mix(SENTIEON_VARCAL_INDEL.out.versions)
+        versions = versions.mix(SENTIEON_APPLYVARCAL_INDEL.out.versions)
     }
 
     versions = versions.mix(SENTIEON_GVCFTYPER.out.versions)
-    versions = versions.mix(SENTIEON_VARCAL_SNP.out.versions)
-    versions = versions.mix(SENTIEON_VARCAL_INDEL.out.versions)
-    versions = versions.mix(SENTIEON_APPLYVARCAL_INDEL.out.versions)
 
     emit:
     genotype_index  // channel: [ val(meta), [ tbi ] ]
diff --git a/subworkflows/local/bam_variant_calling_germline_all/main.nf b/subworkflows/local/bam_variant_calling_germline_all/main.nf
index 666c7c7b6b..5989023adf 100644
--- a/subworkflows/local/bam_variant_calling_germline_all/main.nf
+++ b/subworkflows/local/bam_variant_calling_germline_all/main.nf
@@ -9,12 +9,16 @@ include { BAM_VARIANT_CALLING_DEEPVARIANT         } from '../bam_variant_calling
 include { BAM_VARIANT_CALLING_FREEBAYES           } from '../bam_variant_calling_freebayes/main'
 include { BAM_VARIANT_CALLING_GERMLINE_MANTA      } from '../bam_variant_calling_germline_manta/main'
 include { BAM_VARIANT_CALLING_HAPLOTYPECALLER     } from '../bam_variant_calling_haplotypecaller/main'
+include { BAM_VARIANT_CALLING_SENTIEON_DNASCOPE   } from '../bam_variant_calling_sentieon_dnascope/main'
 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_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'
 
+
+
 workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     take:
     tools                             // Mandatory, list of tools to apply
@@ -41,18 +45,24 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     joint_germline                    // boolean: [mandatory] [default: false] joint calling of germline variants
     skip_haplotypecaller_filter       // boolean: [mandatory] [default: false] whether to filter haplotypecaller single sample vcfs
     sentieon_haplotyper_emit_mode     // channel: [mandatory] value channel with string
+    sentieon_dnascope_emit_mode       // channel: [mandatory] value channel with string
+    sentieon_dnascope_pcr_indel_model // channel: [mandatory] value channel with string
+    sentieon_dnascope_model           // channel: [mandatory] value channel with string
 
     main:
     versions = Channel.empty()
 
     //TODO: Temporary until the if's can be removed and printing to terminal is prevented with "when" in the modules.config
+    gvcf_sentieon_dnascope   = Channel.empty()
+    gvcf_sentieon_haplotyper = Channel.empty()
+
     vcf_deepvariant          = Channel.empty()
     vcf_freebayes            = Channel.empty()
     vcf_haplotypecaller      = Channel.empty()
     vcf_manta                = Channel.empty()
     vcf_mpileup              = Channel.empty()
+    vcf_sentieon_dnascope    = Channel.empty()
     vcf_sentieon_haplotyper  = Channel.empty()
-    gvcf_sentieon_haplotyper = Channel.empty()
     vcf_strelka              = Channel.empty()
     vcf_tiddit               = Channel.empty()
 
@@ -180,6 +190,66 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
         versions = versions.mix(BAM_VARIANT_CALLING_GERMLINE_MANTA.out.versions)
     }
 
+    // SENTIEON DNASCOPE
+    if (tools.split(',').contains('sentieon_dnascope')) {
+        BAM_VARIANT_CALLING_SENTIEON_DNASCOPE(
+            cram,
+            fasta,
+            fasta_fai,
+            dict,
+            dbsnp,
+            dbsnp_tbi,
+            dbsnp_vqsr,
+            intervals,
+            joint_germline,
+            sentieon_dnascope_emit_mode,
+            sentieon_dnascope_pcr_indel_model,
+            sentieon_dnascope_model)
+
+        versions = versions.mix(BAM_VARIANT_CALLING_SENTIEON_DNASCOPE.out.versions)
+
+        vcf_sentieon_dnascope      = BAM_VARIANT_CALLING_SENTIEON_DNASCOPE.out.vcf
+        vcf_tbi_sentieon_dnascope  = BAM_VARIANT_CALLING_SENTIEON_DNASCOPE.out.vcf_tbi
+        gvcf_sentieon_dnascope     = BAM_VARIANT_CALLING_SENTIEON_DNASCOPE.out.gvcf
+        gvcf_tbi_sentieon_dnascope = BAM_VARIANT_CALLING_SENTIEON_DNASCOPE.out.gvcf_tbi
+
+        if (joint_germline) {
+            BAM_JOINT_CALLING_GERMLINE_SENTIEON(
+                BAM_VARIANT_CALLING_SENTIEON_DNASCOPE.out.genotype_intervals,
+                fasta,
+                fasta_fai,
+                dict,
+                dbsnp,
+                dbsnp_tbi,
+                dbsnp_vqsr,
+                known_sites_indels,
+                known_sites_indels_tbi,
+                known_indels_vqsr,
+                known_sites_snps,
+                known_sites_snps_tbi,
+                known_snps_vqsr,
+                'sentieon_dnascope')
+
+            vcf_sentieon_dnascope = BAM_JOINT_CALLING_GERMLINE_SENTIEON.out.genotype_vcf
+            versions = versions.mix(BAM_JOINT_CALLING_GERMLINE_SENTIEON.out.versions)
+        } else {
+            // If single sample track, check if filtering should be done
+            if (!(skip_tools && skip_tools.split(',').contains('dnascope_filter'))) {
+
+                SENTIEON_DNAMODELAPPLY(
+                    vcf_sentieon_dnascope.join(vcf_tbi_sentieon_dnascope, failOnDuplicate: true, failOnMismatch: true),
+                    fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] },
+                    fasta_fai.map{ fai -> [ [ id:fai.baseName ], fai ] },
+                    sentieon_dnascope_model.map{ model -> [ [ id:model.baseName ], model ] })
+
+                vcf_sentieon_dnascope = SENTIEON_DNAMODELAPPLY.out.vcf
+                versions = versions.mix(SENTIEON_DNAMODELAPPLY.out.versions)
+
+            }
+
+        }
+    }
+
     // SENTIEON HAPLOTYPER
     if (tools.split(',').contains('sentieon_haplotyper')) {
         BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER(
@@ -215,7 +285,8 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
                 known_indels_vqsr,
                 known_sites_snps,
                 known_sites_snps_tbi,
-                known_snps_vqsr)
+                known_snps_vqsr,
+                'sentieon_haplotyper')
 
             vcf_sentieon_haplotyper = BAM_JOINT_CALLING_GERMLINE_SENTIEON.out.genotype_vcf
             versions = versions.mix(BAM_JOINT_CALLING_GERMLINE_SENTIEON.out.versions)
@@ -270,6 +341,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     vcf_all = Channel.empty().mix(
         vcf_deepvariant,
         vcf_freebayes,
+        vcf_sentieon_dnascope,
         vcf_haplotypecaller,
         vcf_manta,
         vcf_mpileup,
@@ -279,6 +351,8 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     )
 
     emit:
+    gvcf_sentieon_dnascope
+    gvcf_sentieon_haplotyper
     vcf_all
     vcf_deepvariant
     vcf_freebayes
@@ -286,8 +360,8 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     vcf_manta
     vcf_mpileup
     vcf_strelka
+    vcf_sentieon_dnascope
     vcf_sentieon_haplotyper
-    gvcf_sentieon_haplotyper
     vcf_tiddit
 
     versions
diff --git a/subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf b/subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf
new file mode 100644
index 0000000000..9eea9b2d61
--- /dev/null
+++ b/subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf
@@ -0,0 +1,157 @@
+//
+// SENTIEON HAPLOTYPER germline variant 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 { GATK4_MERGEVCFS            as MERGE_SENTIEON_DNASCOPE_GVCFS } from '../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS            as MERGE_SENTIEON_DNASCOPE_VCFS  } from '../../../modules/nf-core/gatk4/mergevcfs/main'
+include { SENTIEON_DNASCOPE                                           } from '../../../modules/nf-core/sentieon/dnascope/main'
+
+workflow BAM_VARIANT_CALLING_SENTIEON_DNASCOPE {
+    take:
+    cram                              // channel: [mandatory] [ meta, cram, crai, interval.bed ]
+    fasta                             // channel: [mandatory]
+    fasta_fai                         // channel: [mandatory]
+    dict                              // channel: [mandatory]
+    dbsnp                             // channel: [optional]
+    dbsnp_tbi                         // channel: [optional]
+    dbsnp_vqsr                        // channel: [optional]
+    intervals                         // channel: [mandatory] [ intervals, num_intervals ] or [ [], 0 ] if no intervals
+    joint_germline                    // boolean: [mandatory] [default: false] joint calling of germline variants
+    sentieon_dnascope_emit_mode       // string
+    sentieon_dnascope_pcr_indel_model // string
+    sentieon_dnascope_model           // channel
+
+    main:
+    versions = Channel.empty()
+
+    gvcf               = Channel.empty()
+    vcf                = Channel.empty()
+    genotype_intervals = Channel.empty()
+
+    // Combine cram and intervals for spread and gather strategy
+    cram_intervals_for_sentieon = cram.combine(intervals)
+        // Move num_intervals to meta map
+        .map{ meta, cram, crai, intervals, num_intervals -> [
+            meta + [
+                num_intervals:num_intervals,
+                intervals_name:intervals.simpleName,
+                variantcaller:'sentieon_dnascope'],
+            cram,
+            crai,
+            intervals
+            ]
+        }
+
+    emit_mode_items = sentieon_dnascope_emit_mode.split(',').each{ it -> it.toLowerCase().trim() }
+    lst = emit_mode_items - 'gvcf'
+    emit_vcf = lst.size() > 0 ? lst[0] : ''
+
+    SENTIEON_DNASCOPE(
+        cram_intervals_for_sentieon,
+        fasta.map{it -> [[:], it]},
+        fasta_fai.map{it -> [[:], it]},
+        dbsnp.map{it -> [[:], it]},
+        dbsnp_tbi.map{it -> [[:], it]},
+        sentieon_dnascope_model.map{it -> [[:], it]},
+        sentieon_dnascope_pcr_indel_model,
+        emit_vcf,
+        emit_mode_items.any{ it.equals('gvcf') })
+
+    if (joint_germline) {
+        genotype_intervals = SENTIEON_DNASCOPE.out.gvcf
+            .join(SENTIEON_DNASCOPE.out.gvcf_tbi, failOnMismatch: true)
+            .join(cram_intervals_for_sentieon, failOnMismatch: true)
+            .map{ meta, gvcf, tbi, cram, crai, intervals -> [ meta, gvcf, tbi, intervals ] }
+    }
+
+    // Figure out if using intervals or no_intervals
+    dnascope_vcf_branch = SENTIEON_DNASCOPE.out.vcf.map{
+            meta, vcf -> [ meta - meta.subMap('interval_name'), vcf]
+        }
+        .branch{
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }
+
+    dnascope_vcf_tbi_branch = SENTIEON_DNASCOPE.out.vcf_tbi.map{
+            meta, vcf_tbi -> [ meta - meta.subMap('interval_name'), vcf_tbi]
+        }
+        .branch{
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }
+
+    haplotyper_gvcf_branch = SENTIEON_DNASCOPE.out.gvcf.map{
+            meta, gvcf -> [ meta - meta.subMap('interval_name'), gvcf]
+        }
+        .branch{
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }
+
+    haplotyper_gvcf_tbi_branch = SENTIEON_DNASCOPE.out.gvcf_tbi.map{
+            meta, gvcf_tbi -> [ meta - meta.subMap('interval_name'), gvcf_tbi]
+        }
+        .branch{
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }
+
+    vcfs_for_merging = dnascope_vcf_branch.intervals.map{
+        meta, vcf -> [ groupKey(meta, meta.num_intervals), vcf ]}
+
+    vcfs_for_merging = vcfs_for_merging.map{
+        meta, vcf -> [
+            meta - meta.subMap('intervals_name'),
+            vcf]}.groupTuple()
+
+    // VCFs
+    // Only when using intervals
+    MERGE_SENTIEON_DNASCOPE_VCFS(vcfs_for_merging, dict)
+
+    dnascope_vcf = Channel.empty().mix(
+        MERGE_SENTIEON_DNASCOPE_VCFS.out.vcf,
+        dnascope_vcf_branch.no_intervals)
+
+    haplotyper_tbi = Channel.empty().mix(
+        MERGE_SENTIEON_DNASCOPE_VCFS.out.tbi,
+        dnascope_vcf_tbi_branch.no_intervals)
+
+    // Remove no longer necessary field: num_intervals
+    vcf = dnascope_vcf.map{ meta, vcf -> [ meta - meta.subMap('num_intervals'), vcf ] }
+    vcf_tbi = haplotyper_tbi.map{ meta, tbi -> [ meta - meta.subMap('num_intervals'), tbi ] }
+
+    // GVFs
+    // Only when using intervals
+    gvcfs_for_merging = haplotyper_gvcf_branch.intervals.map{
+        meta, vcf -> [groupKey(meta, meta.num_intervals), vcf]}
+
+    gvcfs_for_merging = gvcfs_for_merging.map{
+        meta, vcf -> [ meta - meta.subMap('intervals_name'), vcf ]
+    }.groupTuple()
+
+    MERGE_SENTIEON_DNASCOPE_GVCFS(gvcfs_for_merging, dict)
+
+    gvcf = Channel.empty().mix(
+        MERGE_SENTIEON_DNASCOPE_GVCFS.out.vcf,
+        haplotyper_gvcf_branch.no_intervals)
+
+    gvcf_tbi = Channel.empty().mix(
+        MERGE_SENTIEON_DNASCOPE_GVCFS.out.tbi,
+        haplotyper_gvcf_tbi_branch.no_intervals)
+
+    versions = versions.mix(SENTIEON_DNASCOPE.out.versions)
+    versions = versions.mix(MERGE_SENTIEON_DNASCOPE_VCFS.out.versions)
+    versions = versions.mix(MERGE_SENTIEON_DNASCOPE_GVCFS.out.versions)
+
+    emit:
+    versions
+    vcf
+    vcf_tbi
+    gvcf
+    gvcf_tbi
+    genotype_intervals // For joint genotyping
+
+}
diff --git a/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf b/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
index cf9bcf9e21..4b280d271c 100644
--- a/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
+++ b/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
@@ -42,7 +42,8 @@ workflow BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER {
             ]
         }
 
-    emit_mode_items = sentieon_haplotyper_emit_mode.split(',')
+
+    emit_mode_items = sentieon_haplotyper_emit_mode.split(',').each{ it -> it.toLowerCase().trim() }
     lst = emit_mode_items - 'gvcf'
     emit_vcf = lst.size() > 0 ? lst[0] : ''
 
@@ -53,7 +54,7 @@ workflow BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER {
         dbsnp,
         dbsnp_tbi,
         emit_vcf,
-        emit_mode_items.contains('gvcf'))
+        emit_mode_items.any{ it.equals('gvcf') })
 
     if (joint_germline) {
         genotype_intervals = SENTIEON_HAPLOTYPER.out.gvcf
diff --git a/tests/config/tags.yml b/tests/config/tags.yml
index 362bc525b9..4fabc3a7d5 100644
--- a/tests/config/tags.yml
+++ b/tests/config/tags.yml
@@ -314,6 +314,31 @@ haplotypecaller_skip_filter:
   - tests/csv/3.0/mapped_single_bam.csv
   - tests/test_haplotypecaller_skip_filter.yml
 
+## sentieon/dnascope
+sentieon/dnascope:
+  - conf/modules/sentieon_dnascope.config
+  - modules/nf-core/sentieon/dnascope/main.nf
+  - modules/nf-core/gatk4/mergevcfs/main.nf
+  - modules/nf-core/samtools/index/main.nf
+  - modules/nf-core/samtools/merge/main.nf
+  - subworkflows/local/bam_merge_index_samtools/main.nf
+  - subworkflows/local/bam_variant_calling_germline_all/main.nf
+  - subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf
+  - tests/csv/3.0/mapped_single_bam.csv
+  - tests/test_sentieon_dnascope.yml
+
+sentieon_dnascope_skip_filter:
+  - conf/modules/sentieon_dnascope.config
+  - modules/nf-core/sentieon/dnascope/main.nf
+  - modules/nf-core/gatk4/mergevcfs/main.nf
+  - modules/nf-core/samtools/index/main.nf
+  - modules/nf-core/samtools/merge/main.nf
+  - subworkflows/local/bam_merge_index_samtools/main.nf
+  - subworkflows/local/bam_variant_calling_germline_all/main.nf
+  - subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf
+  - tests/csv/3.0/mapped_single_bam.csv
+  - tests/test_sentieon_dnascope_skip_filter.yml
+
 ## sentieon/haplotyper
 sentieon/haplotyper:
   - conf/modules/sentieon_haplotyper.config
@@ -364,16 +389,27 @@ joint_germline:
   - tests/csv/3.0/mapped_joint_bam.csv
   - tests/test_joint_germline.yml
 
-## sentieon_joint_germline
-sentieon_joint_germline:
+## sentieon_dnascope_joint_germline
+sentieon_dnascope_joint_germline:
+  - conf/modules/prepare_genome.config
+  - conf/modules/sentieon_dnascope.config
+  - conf/modules/sentieon_dnascope_joint_germline.config
+  - modules/nf-core/sentieon/dnascope/main.nf
+  - subworkflows/local/bam_variant_calling_germline_all/main.nf
+  - subworkflows/local/bam_variant_calling_sentieon_dnascope/main.nf
+  - tests/csv/3.0/mapped_joint_bam.csv
+  - tests/test_sentieon_dnascop_joint_germline.yml
+
+## sentieon_haplotyper_joint_germline
+sentieon_haplotyper_joint_germline:
   - conf/modules/prepare_genome.config
   - conf/modules/sentieon_haplotyper.config
-  - conf/modules/sentieon_joint_germline.config
+  - conf/modules/sentieon_haplotyper_joint_germline.config
   - modules/nf-core/sentieon/haplotyper/main.nf
   - subworkflows/local/bam_variant_calling_germline_all/main.nf
   - subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
   - tests/csv/3.0/mapped_joint_bam.csv
-  - tests/test_sentieon_joint_germline.yml
+  - tests/test_sentieon_haplotyper_joint_germline.yml
 
 ## manta
 manta:
diff --git a/tests/test_gatk4_spark.yml b/tests/test_gatk4_spark.yml
index 32082446ec..8dbc8fb974 100644
--- a/tests/test_gatk4_spark.yml
+++ b/tests/test_gatk4_spark.yml
@@ -48,7 +48,7 @@
     # conda changes md5sums for test
     - path: results/preprocessing/mapped/
       should_exist: false
-- name: Run default pipeline with gatk4_spark & skipping all QC steps
+- name: Run default pipeline with gatk4_spark and skipping all QC steps
   command: nextflow run main.nf -profile test_cache,use_gatk_spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results
   tags:
     - gatk4_spark
diff --git a/tests/test_sentieon_dnascope.yml b/tests/test_sentieon_dnascope.yml
new file mode 100644
index 0000000000..f51e0bca72
--- /dev/null
+++ b/tests/test_sentieon_dnascope.yml
@@ -0,0 +1,147 @@
+- name: Run variant calling on germline sample with sentieons dnascope
+  command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results
+  tags:
+    - germline
+    - sentieon/dnascope
+    - variant_calling
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: b2144d21a0ebfd807a8646f1751d0ddc
+    - path: results/multiqc
+    - path: results/preprocessing/converted/test/test.converted.cram
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/converted/test/test.converted.cram.crai
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/sentieon_dnascope/test/test.dnascope.filtered.bcftools_stats.txt
+      md5sum: 912c7d5b31784c50e0a75b4fcfa4997b
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.FILTER.summary
+      md5sum: e67b24d296810a075378e5864bcea0fa
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.TsTv.count
+      md5sum: b77c120ee5cc0423267200c67d60c663
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.TsTv.qual
+      # changes md5sum on reruns. This is somewhat unexpected, but might to tiny variation in very small numbers in the qual-files.
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/dnascope
+      should_exist: false
+- name: Run variant calling on germline sample with sentieons dnascope without intervals
+  command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --no_intervals --outdir results
+  tags:
+    - germline
+    - sentieon/dnascope
+    - no_intervals
+    - variant_calling
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: b2144d21a0ebfd807a8646f1751d0ddc
+    - path: results/multiqc
+    - path: results/no_intervals.bed
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/no_intervals.bed.gz
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/no_intervals.bed.gz.tbi
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/preprocessing/converted/test/test.converted.cram
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/converted/test/test.converted.cram.crai
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/sentieon_dnascope/test/test.dnascope.filtered.bcftools_stats.txt
+      md5sum: 912c7d5b31784c50e0a75b4fcfa4997b
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.FILTER.summary
+      md5sum: e67b24d296810a075378e5864bcea0fa
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.TsTv.count
+      md5sum: b77c120ee5cc0423267200c67d60c663
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.TsTv.qual
+      # changes md5sum on reruns. This is somewhat unexpected, but might to tiny variation in very small numbers in the qual-files.
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/sentieon_dnascope
+      should_exist: false
+- name: Run variant calling on germline sample with sentieons dnascope output gvcf
+  command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode gvcf
+  tags:
+    - germline
+    - sentieon/dnascope
+    - variant_calling
+  files:
+    - path: results/csv/variantcalled.csv
+      should_exist: false
+    - path: results/multiqc
+    - path: results/preprocessing/converted/test/test.converted.cram
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/converted/test/test.converted.cram.crai
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/sentieon_dnascope/test/test.dnascope.filtered.bcftools_stats.txt
+      should_exist: false
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.FILTER.summary
+      should_exist: false
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.TsTv.count
+      should_exist: false
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.TsTv.qual
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.g.vcf.gz
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.g.vcf.gz.tbi
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz.tbi
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz.tbi
+      should_exist: false
+    - path: results/dnascope
+      should_exist: false
+- name: Run variant calling on germline sample with sentieons dnascope output both gvcf and vcf
+  command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode variant,gvcf
+  tags:
+    - germline
+    - sentieon/dnascope
+    - variant_calling
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: b2144d21a0ebfd807a8646f1751d0ddc
+    - path: results/multiqc
+    - path: results/preprocessing/converted/test/test.converted.cram
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/converted/test/test.converted.cram.crai
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/sentieon_dnascope/test/test.dnascope.filtered.bcftools_stats.txt
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.FILTER.summary
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.TsTv.count
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.filtered.TsTv.qual
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.g.vcf.gz
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.g.vcf.gz.tbi
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz.tbi
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz.tbi
+    - path: results/dnascope
+      should_exist: false
diff --git a/tests/test_sentieon_dnascope_joint_germline.yml b/tests/test_sentieon_dnascope_joint_germline.yml
new file mode 100644
index 0000000000..e905b9cd53
--- /dev/null
+++ b/tests/test_sentieon_dnascope_joint_germline.yml
@@ -0,0 +1,68 @@
+- name: Run joint germline variant calling with sentieon dnascope
+  command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf
+  tags:
+    - germline
+    - sentieon_dnascope_joint_germline
+    - variant_calling
+    - sentieon/dnascope
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: 62d70060aad96337254efe2d7a1df170
+    - path: results/multiqc
+    - path: results/reports/bcftools/sentieon_dnascope/joint_variant_calling/joint_germline.bcftools_stats.txt
+    - path: results/reports/vcftools/sentieon_dnascope/joint_variant_calling/joint_germline.FILTER.summary
+    - path: results/reports/vcftools/sentieon_dnascope/joint_variant_calling/joint_germline.TsTv.count
+    - path: results/reports/vcftools/sentieon_dnascope/joint_variant_calling/joint_germline.TsTv.qual
+    - path: results/variant_calling/sentieon_dnascope/joint_variant_calling/joint_germline.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/joint_variant_calling/joint_germline.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/testN/testN.dnascope.g.vcf.gz
+    - path: results/variant_calling/sentieon_dnascope/testN/testN.dnascope.g.vcf.gz.tbi
+    - path: results/variant_calling/sentieon_dnascope/testT/testT.dnascope.g.vcf.gz
+    - path: results/variant_calling/sentieon_dnascope/testT/testT.dnascope.g.vcf.gz.tbi
+    - path: results/dnascope
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/sentieon_dnascope/joint_variant_calling/joint_germline_recalibrated.bcftools_stats.txt
+      should_exist: false
+    - path: results/reports/vcftools/sentieon_dnascope/joint_variant_calling/joint_germline_recalibrated.FILTER.summary
+      should_exist: false
+    - path: results/reports/vcftools/sentieon_dnascope/joint_variant_calling/joint_germline_recalibrated.TsTv.count
+      should_exist: false
+    - path: results/reports/vcftools/sentieon_dnascope/joint_variant_calling/joint_germline_recalibrated.TsTv.qual
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/joint_variant_calling/joint_germline_recalibrated.vcf.gz
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/joint_variant_calling/joint_germline_recalibrated.vcf.gz.tbi
+      should_exist: false
+- name: Run joint germline variant calling with sentieon dnascope all intervals at once
+  command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf --nucleotides_per_second 100
+  tags:
+    - germline
+    - sentieon_dnascope_joint_germline
+    - variant_calling
+    - sentieon/dnascope
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: 62d70060aad96337254efe2d7a1df170
+    - path: results/multiqc
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/sentieon_dnascope/joint_variant_calling/joint_germline.bcftools_stats.txt
+    - path: results/reports/vcftools/sentieon_dnascope/joint_variant_calling/joint_germline.FILTER.summary
+    - path: results/reports/vcftools/sentieon_dnascope/joint_variant_calling/joint_germline.TsTv.count
+    - path: results/reports/vcftools/sentieon_dnascope/joint_variant_calling/joint_germline.TsTv.qual
+    - path: results/variant_calling/sentieon_dnascope/joint_variant_calling/joint_germline.vcf.gz
+    - path: results/variant_calling/sentieon_dnascope/joint_variant_calling/joint_germline.vcf.gz.tbi
+    - path: results/variant_calling/sentieon_dnascope/testN/testN.dnascope.g.vcf.gz
+    - path: results/variant_calling/sentieon_dnascope/testN/testN.dnascope.g.vcf.gz.tbi
+    - path: results/variant_calling/sentieon_dnascope/testT/testT.dnascope.g.vcf.gz
+    - path: results/variant_calling/sentieon_dnascope/testT/testT.dnascope.g.vcf.gz.tbi
+    - path: results/dnascope
+      should_exist: false
diff --git a/tests/test_sentieon_dnascope_skip_filter.yml b/tests/test_sentieon_dnascope_skip_filter.yml
new file mode 100644
index 0000000000..16bbca9e7c
--- /dev/null
+++ b/tests/test_sentieon_dnascope_skip_filter.yml
@@ -0,0 +1,81 @@
+- name: Run variant calling on germline sample with sentieon dnascope and skip filter
+  command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --outdir results
+  tags:
+    - germline
+    - sentieon_dnascope_skip_filter
+    - variant_calling
+    - sentieon/dnascope
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: 10254414c0679ba1fb25e41b9ff548cc
+    - path: results/multiqc
+    - path: results/preprocessing/converted/test/test.converted.cram
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/converted/test/test.converted.cram.crai
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/sentieon_dnascope/test/test.dnascope.unfiltered.bcftools_stats.txt
+      md5sum: f915fe1591ababb0da5e7b43dfc35092
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.unfiltered.FILTER.summary
+      md5sum: 87a84b5f8ac3d3cbeeef7d60afcdbfe7
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.unfiltered.TsTv.count
+      md5sum: b77c120ee5cc0423267200c67d60c663
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.unfiltered.TsTv.qual
+      # changes md5sum on reruns. This is somewhat unexpected, but might to tiny variation in very small numbers in the qual-files.
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz.tbi
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/sentieon_dnascope
+      should_exist: false
+- name: Run variant calling on germline sample with sentieon dnascope without intervals and skip filter
+  command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --no_intervals --outdir results
+  tags:
+    - germline
+    - sentieon_dnascope_skip_filter
+    - no_intervals
+    - variant_calling
+    - sentieon/dnascope
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: 10254414c0679ba1fb25e41b9ff548cc
+    - path: results/multiqc
+    - path: results/no_intervals.bed
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/no_intervals.bed.gz
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/no_intervals.bed.gz.tbi
+      md5sum: f3dac01ea66b95fe477446fde2d31489
+    - path: results/preprocessing/converted/test/test.converted.cram
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/converted/test/test.converted.cram.crai
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/sentieon_dnascope/test/test.dnascope.unfiltered.bcftools_stats.txt
+      md5sum: f915fe1591ababb0da5e7b43dfc35092
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.unfiltered.FILTER.summary
+      md5sum: 87a84b5f8ac3d3cbeeef7d60afcdbfe7
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.unfiltered.TsTv.count
+      md5sum: b77c120ee5cc0423267200c67d60c663
+    - path: results/reports/vcftools/sentieon_dnascope/test/test.dnascope.unfiltered.TsTv.qual
+      # changes md5sum on reruns. This is somewhat unexpected, but might to tiny variation in very small numbers in the qual-files.
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.filtered.vcf.gz.tbi
+      should_exist: false
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/sentieon_dnascope
+      should_exist: false
diff --git a/tests/test_sentieon_joint_germline.yml b/tests/test_sentieon_haplotyper_joint_germline.yml
similarity index 97%
rename from tests/test_sentieon_joint_germline.yml
rename to tests/test_sentieon_haplotyper_joint_germline.yml
index 4637571aec..1c12f101db 100644
--- a/tests/test_sentieon_joint_germline.yml
+++ b/tests/test_sentieon_haplotyper_joint_germline.yml
@@ -2,7 +2,7 @@
   command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf
   tags:
     - germline
-    - sentieon_joint_germline
+    - sentieon_haplotyper_joint_germline
     - variant_calling
     - sentieon/haplotyper
   files:
@@ -31,7 +31,7 @@
   command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100
   tags:
     - germline
-    - sentieon_joint_germline
+    - sentieon_haplotyper_joint_germline
     - variant_calling
     - sentieon/haplotyper
   files:
@@ -58,7 +58,7 @@
   command: nextflow run main.nf -profile test_cache,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run
   tags:
     - germline
-    - sentieon_joint_germline
+    - sentieon_haplotyper_joint_germline
     - variant_calling
     - vqsr
   files:
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index 5ae80fbae1..a6ed5b2e50 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -50,6 +50,8 @@ def checkPathParamList = [
     params.multiqc_config,
     params.pon,
     params.pon_tbi,
+    params.sentieon_dnascope_model,
+    params.snpeff_cache,
     params.spliceai_indel,
     params.spliceai_indel_tbi,
     params.spliceai_snv,
@@ -255,18 +257,60 @@ if (!params.dbsnp && !params.known_indels) {
     if (params.step in ['mapping', 'markduplicates', 'prepare_recalibration', 'recalibrate'] && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('baserecalibrator')))) {
         error("Base quality score recalibration requires at least one resource file. Please provide at least one of `--dbsnp` or `--known_indels`\nYou can skip this step in the workflow by adding `--skip_tools baserecalibrator` to the command.")
     }
-    if (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper'))) {
-        log.warn "If GATK's Haplotypecaller or Sentieon's Haplotyper is specified, without `--dbsnp` or `--known_indels no filtering will be done. For filtering, please provide at least one of `--dbsnp` or `--known_indels`.\nFor more information see FilterVariantTranches (single-sample, default): https://gatk.broadinstitute.org/hc/en-us/articles/5358928898971-FilterVariantTranches\nFor more information see VariantRecalibration (--joint_germline): https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator\nFor more information on GATK Best practice germline variant calling: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-"
+    if (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope'))) {
+        log.warn "If GATK's Haplotypecaller, Sentieon's Dnascpe or Sentieon's Haplotyper is specified, without `--dbsnp` or `--known_indels no filtering will be done. For filtering, please provide at least one of `--dbsnp` or `--known_indels`.\nFor more information see FilterVariantTranches (single-sample, default): https://gatk.broadinstitute.org/hc/en-us/articles/5358928898971-FilterVariantTranches\nFor more information see VariantRecalibration (--joint_germline): https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator\nFor more information on GATK Best practice germline variant calling: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-"
     }
 }
-if (params.joint_germline && (!params.tools || !(params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper')))) {
-    error("The GATK's Haplotypecaller or Sentieon's Haplotyper should be specified as one of the tools when doing joint germline variant calling.) ")
+if (params.joint_germline && (!params.tools || !(params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope')))) {
+    error("The GATK's Haplotypecaller, Sentieon's Dnascope or Sentieon's Haplotyper should be specified as one of the tools when doing joint germline variant calling.) ")
 }
 
-if (params.joint_germline && (!params.dbsnp || !params.known_indels || !params.known_snps || params.no_intervals)) {
-    log.warn "If GATK's Haplotypecaller or Sentieon's Haplotyper is specified, without `--dbsnp`, `--known_snps`, `--known_indels` or the associated resource labels (ie `known_snps_vqsr`), no variant recalibration will be done. For recalibration you must provide all of these resources.\nFor more information see VariantRecalibration: https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator \nJoint germline variant calling also requires intervals in order to genotype the samples. As a result, if `--no_intervals` is set to `true` the joint germline variant calling will not be performed."
+if (
+    params.tools &&
+    (
+        params.tools.split(',').contains('haplotypecaller') ||
+        params.tools.split(',').contains('sentieon_haplotyper') ||
+        params.tools.split(',').contains('sentieon_dnascope')
+    ) &&
+    params.joint_germline &&
+    (
+        !params.dbsnp ||
+        !params.known_indels ||
+        !params.known_snps ||
+        params.no_intervals
+    )
+    ) {
+    log.warn("""If GATK's Haplotypecaller, Sentieon's Dnascope and/or Sentieon's Haplotyper is specified, \
+but without `--dbsnp`, `--known_snps`, `--known_indels` or the associated resource labels (ie `known_snps_vqsr`), \
+no variant recalibration will be done. For recalibration you must provide all of these resources.\nFor more information \
+see VariantRecalibration: https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator \n\
+Joint germline variant calling also requires intervals in order to genotype the samples. \
+As a result, if `--no_intervals` is set to `true` the joint germline variant calling will not be performed.""")
 }
 
+if (params.tools &&
+    params.tools.split(',').contains('sentieon_dnascope') &&
+    params.joint_germline &&
+    (
+        !params.sentieon_dnascope_emit_mode ||
+        !params.sentieon_dnascope_emit_mode.split(',').contains('gvcf')
+    )
+    ) {
+    error("When using Sentieon Dnascope for joint-germline variant-calling the option `--sentieon_dnascope_emit_mode` has to include `gvcf`.")
+}
+
+if (params.tools &&
+    params.tools.split(',').contains('sentieon_haplotyper') &&
+    params.joint_germline &&
+    (
+        !params.sentieon_haplotyper_emit_mode ||
+        !params.sentieon_haplotyper_emit_mode.split(',').contains('gvcf')
+    )
+    ) {
+    error("When using Sentieon Haplotyper for joint-germline variant-calling the option `--sentieon_haplotyper_emit_mode` has to include `gvcf`.")
+}
+
+
 // Fails when --joint_mutect2 is used without enabling mutect2
 if (params.joint_mutect2 && (!params.tools || !params.tools.split(',').contains('mutect2'))) {
     error("The mutect2 should be specified as one of the tools when doing joint somatic variant calling with Mutect2. (The mutect2 could be specified by adding `--tools mutect2` to the nextflow command.)")
@@ -297,20 +341,21 @@ if ((params.download_cache) && (params.snpeff_cache || params.vep_cache)) {
 */
 
 // Initialize file channels based on params, defined in the params.genomes[params.genome] scope
-ascat_alleles      = params.ascat_alleles      ? Channel.fromPath(params.ascat_alleles).collect()     : Channel.empty()
-ascat_loci         = params.ascat_loci         ? Channel.fromPath(params.ascat_loci).collect()        : Channel.empty()
-ascat_loci_gc      = params.ascat_loci_gc      ? Channel.fromPath(params.ascat_loci_gc).collect()     : Channel.value([])
-ascat_loci_rt      = params.ascat_loci_rt      ? Channel.fromPath(params.ascat_loci_rt).collect()     : Channel.value([])
-cf_chrom_len       = params.cf_chrom_len       ? Channel.fromPath(params.cf_chrom_len).collect()      : []
-chr_dir            = params.chr_dir            ? Channel.fromPath(params.chr_dir).collect()           : Channel.value([])
-dbsnp              = params.dbsnp              ? Channel.fromPath(params.dbsnp).collect()             : Channel.value([])
-fasta              = params.fasta              ? Channel.fromPath(params.fasta).first()               : Channel.empty()
-fasta_fai          = params.fasta_fai          ? Channel.fromPath(params.fasta_fai).collect()         : Channel.empty()
-germline_resource  = params.germline_resource  ? Channel.fromPath(params.germline_resource).collect() : Channel.value([]) // Mutect2 does not require a germline resource, so set to optional input
-known_indels       = params.known_indels       ? Channel.fromPath(params.known_indels).collect()      : Channel.value([])
-known_snps         = params.known_snps         ? Channel.fromPath(params.known_snps).collect()        : Channel.value([])
-mappability        = params.mappability        ? Channel.fromPath(params.mappability).collect()       : Channel.value([])
-pon                = params.pon                ? Channel.fromPath(params.pon).collect()               : Channel.value([]) // PON is optional for Mutect2 (but highly recommended)
+ascat_alleles           = params.ascat_alleles           ? Channel.fromPath(params.ascat_alleles).collect()           : Channel.empty()
+ascat_loci              = params.ascat_loci              ? Channel.fromPath(params.ascat_loci).collect()              : Channel.empty()
+ascat_loci_gc           = params.ascat_loci_gc           ? Channel.fromPath(params.ascat_loci_gc).collect()           : Channel.value([])
+ascat_loci_rt           = params.ascat_loci_rt           ? Channel.fromPath(params.ascat_loci_rt).collect()           : Channel.value([])
+cf_chrom_len            = params.cf_chrom_len            ? Channel.fromPath(params.cf_chrom_len).collect()            : []
+chr_dir                 = params.chr_dir                 ? Channel.fromPath(params.chr_dir).collect()                 : Channel.value([])
+dbsnp                   = params.dbsnp                   ? Channel.fromPath(params.dbsnp).collect()                   : Channel.value([])
+fasta                   = params.fasta                   ? Channel.fromPath(params.fasta).first()                     : Channel.empty()
+fasta_fai               = params.fasta_fai               ? Channel.fromPath(params.fasta_fai).collect()               : Channel.empty()
+germline_resource       = params.germline_resource       ? Channel.fromPath(params.germline_resource).collect()       : Channel.value([]) // Mutect2 does not require a germline resource, so set to optional input
+known_indels            = params.known_indels            ? Channel.fromPath(params.known_indels).collect()            : Channel.value([])
+known_snps              = params.known_snps              ? Channel.fromPath(params.known_snps).collect()              : Channel.value([])
+mappability             = params.mappability             ? Channel.fromPath(params.mappability).collect()             : Channel.value([])
+pon                     = params.pon                     ? Channel.fromPath(params.pon).collect()                     : Channel.value([]) // PON is optional for Mutect2 (but highly recommended)
+sentieon_dnascope_model = params.sentieon_dnascope_model ? Channel.fromPath(params.sentieon_dnascope_model).collect() : Channel.value([])
 
 // Initialize value channels based on params, defined in the params.genomes[params.genome] scope
 ascat_genome       = params.ascat_genome       ?: Channel.empty()
@@ -1164,7 +1209,10 @@ workflow SAREK {
             known_snps_vqsr,
             params.joint_germline,
             params.skip_tools && params.skip_tools.split(',').contains('haplotypecaller_filter'), // true if filtering should be skipped
-            params.sentieon_haplotyper_emit_mode)
+            params.sentieon_haplotyper_emit_mode,
+            params.sentieon_dnascope_emit_mode,
+            params.sentieon_dnascope_pcr_indel_model,
+            sentieon_dnascope_model)
 
         // TUMOR ONLY VARIANT CALLING
         BAM_VARIANT_CALLING_TUMOR_ONLY_ALL(
@@ -1232,6 +1280,7 @@ workflow SAREK {
         vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_freebayes)
         vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_haplotypecaller)
         vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_manta)
+        vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_sentieon_dnascope)
         vcf_to_annotate = vcf_to_annotate.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_sentieon_haplotyper)
         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)