# Supported variant callers

Emedgene provides the tightest integration with DRAGEN for germline variation analysis, providing accuracy, comprehensiveness, and efficiency, spanning variant calling through interpretation and report generation.

### Compatibility with DRAGEN and DRAGEN Array Variant Callers

| DRAGEN version                                                                                                                                                                                                 | Emedgene version | Available callers                                           |
| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------- | ----------------------------------------------------------- |
| <p>4.4<br><a href="https://github.com/illumina-swi/emedgene-docs/blob/prod/docs/release-notes/workbench-and-pipeline-updates/new-in-emedgene-v100.39.0-october-16th-2025">See full compatibility table</a></p> | 100.39.0+        | SNV, CNV, STR, SV (del/dup/ins), Targeted, MRJD, Ploidy     |
| <p>4.3<br><a href="../../release-notes/workbench-and-pipeline-updates/new_in_emedgene_36_-october_8th_2024#general-compatibility-with-dragen-4.3-variant-callers">See full compatibility table</a></p>         | 36.0+            | SNV, CNV, STR, SV (del/dup/ins), Targeted, MRJD, JSON PGx\* |
| <p>4.2<br><a href="../release-notes/workbench-and-pipeline-updates/more-release-notes/new_in_emedgene_35_-may_22nd_2024">See full compatibility table</a></p>                                                  | All              | SNV, CNV, STR, SV (del/dup/ins), SMN, JSON PGx\*            |
| 4.2                                                                                                                                                                                                            | All              | SNV, CNV, STR, SV (del/dup/ins), SMN                        |
| 4.0                                                                                                                                                                                                            | All              | SNV, CNV, STR, SV (del/dup/ins)                             |
| 3.10                                                                                                                                                                                                           | All              | SNV, CNV, STR, SV (del/dup/ins)                             |
| 3.6-3.9                                                                                                                                                                                                        | All              | SNV                                                         |

***

| DRAGEN Array version | Emedgene version | Available callers |
| -------------------- | ---------------- | ----------------- |
| 1.3                  | 100.39.0+        | Cyto              |
| 1.2                  | 37.0+            | Cyto              |

### Extensive Compatibility with Additional Variant Callers

The Emedgene platform supports a variety of variant callers and applies specific quality parameters for each. The quality assessment is an essential step in the Emedgene pipeline because variants with low quality will not be considered by the AI components.

If the variant caller is not supported or not recognized, a default quality function will be applied. The default parameters are built on GT (genotype), depth (DP) and allele bias (AB). These fields are mandatory, and their absence will induce “Low quality” for all variants.

The following variant callers are currently supported on the Emedgene pipeline, providing a header with the variant caller command line should be present within the VCF headers.

{% hint style="info" %}
Internally, this list is referred to as the Emedgenizers list.\
An Emedgenizer is a tool that normalizes VCF files to the system’s expected format for each variant caller.
{% endhint %}

Additional callers can be supported on demand under license.

<table><thead><tr><th width="196">Variant caller / VCF</th><th width="175">Supported versions</th><th width="202">Notes</th><th>Calling methodology</th></tr></thead><tbody><tr><td><a href="https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ChAS_Manual.pdf#page=469">AED</a> CNV</td><td>N/A</td><td>Affymetrix Extensible Data. converted to VCF</td><td>CNVReadDepth</td></tr><tr><td><a href="https://www.ampliseq.com/">ION AMPLISEQ</a></td><td>5.12, 5.20</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://www.hgsc.bcm.edu/software/atlas-2">Atlas-SNP2</a></td><td>N/A</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/Illumina/canvas">CanvasCNV</a></td><td>1.38</td><td></td><td>CNVReadDepth</td></tr><tr><td>Clair3</td><td></td><td>v37.0+</td><td>SmallVariant</td></tr><tr><td><a href="https://www.qiagen.com/us/products/discovery-and-translational-research/next-generation-sequencing/clc-genomics-workbench/">QIAGEN CLC Genomics Workbench</a></td><td>N/A</td><td></td><td>SmallVariant</td></tr><tr><td>ClinSV</td><td>N/A</td><td></td><td>SVSplitEnd</td></tr><tr><td><a href="https://cnvkit.readthedocs.io/en/stable/">CNVKit</a></td><td>N/A</td><td></td><td>CNVReadDepth</td></tr><tr><td>CNVReporter</td><td>0.01</td><td></td><td>CNVReadDepth</td></tr><tr><td><a href="https://atgu.mgh.harvard.edu/xhmm/">CnvXhmm</a></td><td>1.0</td><td></td><td>CNVReadDepth</td></tr><tr><td><a href="https://github.com/abyzovlab/CNVnator">CNVnator</a></td><td>N/A</td><td></td><td>CNVReadDepth</td></tr><tr><td>cuteSV</td><td>2.02</td><td>v37.0+</td><td>SVSplitEnd</td></tr><tr><td><a href="https://www.thermofisher.com/order/catalog/product/901808">CytoScanHDArray</a></td><td>Multi-Sample Viewer:1.0.0.71</td><td></td><td>Unknown</td></tr><tr><td><a href="https://github.com/google/deepvariant">DeepVariant</a></td><td>1.0.0</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/dooguypapua/eKLIPse">eKLIPse</a></td><td>N/A</td><td></td><td>SVSplitEnd</td></tr><tr><td><a href="https://github.com/vplagnol/ExomeDepth">ExomeDepth</a></td><td>0.1</td><td></td><td>CNVReadDepth</td></tr><tr><td>ExomeDepthAM</td><td>0.1</td><td>Private fork of ExomeDepth</td><td>CNVReadDepth</td></tr><tr><td><a href="https://github.com/freebayes/freebayes">Freebayes</a></td><td>N/A</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://gatk.broadinstitute.org/hc/en-us">GATK</a></td><td>3, 3.4, 3.5, 2014, 4, 4.1</td><td></td><td>SmallVariant</td></tr><tr><td>GATK<a href="https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-MuTect2"> Mutect</a></td><td>N/A</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/GeneDx/scramble">GATKScramble</a></td><td>Scramble</td><td>Running: scramble2vcf.pl</td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/dnanexus-rnd/GLnexus">GLNEXUSSNV</a></td><td>1.4</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/iontorrent">IONTorrent</a></td><td>4.x, 5.x and not: 5.12, 5.20</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/iontorrent">IONTorrent</a> CNV</td><td>5.16</td><td></td><td>CNVReadDepth</td></tr><tr><td><a href="https://melt.igs.umaryland.edu/">MELT</a></td><td>2.2.0</td><td></td><td>SVSplitEnd</td></tr><tr><td><a href="https://github.com/KCCG/mity">Mity</a></td><td>N/A</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://softgenetics.com">NextGene</a></td><td>2.X</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://pypi.org/project/cuteSV/">cuteSV for ONT</a></td><td>2.1.1</td><td></td><td>SVSplitEnd</td></tr><tr><td><a href="https://github.com/EichlerLab/pav">PAV</a></td><td>2.2.4</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/EichlerLab/pav">PAVSV</a></td><td>2.2.4</td><td></td><td>SVSplitEnd</td></tr><tr><td><a href="https://github.com/PacificBiosciences/pbsv">PBSV</a></td><td>2.X</td><td></td><td>SVSplitEnd</td></tr><tr><td><a href="https://github.com/Illumina/Pisces">Pisces</a></td><td>5.2.9</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://www.sentieon.com/">Sentieon</a></td><td>201808, 201911, 202010</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://www.sentieon.com/products/">SentieonDNAScope</a></td><td>201808.03</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/fritzsedlazeck/Sniffles">Sniffles</a></td><td>2.0.6, 2.0.7, 2.5</td><td></td><td>SVSplitEnd</td></tr><tr><td><a href="https://www.sophiagenetics.com/">Sophia</a></td><td>0.0.2</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://www.sophiagenetics.com/">SophiaCnv</a></td><td>2.0.1</td><td></td><td>CNVReadDepth</td></tr><tr><td>Spectre</td><td></td><td>v37.0+</td><td>CNVReadDepth</td></tr><tr><td><a href="https://support.illumina.com/help/BS_App_TS_Amplicon_OLH_15055858/Content/Source/Informatics/Apps/IsaacVariantCaller_appENR.htm">Starling</a></td><td>2.4.5</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/Illumina/strelka">Strelka</a></td><td>N/A</td><td></td><td>SmallVariant</td></tr><tr><td><a href="https://github.com/Illumina/witty.er">Witty</a></td><td>N/A</td><td></td><td>SVSplitEnd</td></tr></tbody></table>