> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/manually-add-variant-from-igv.md).

# Adding variants to a case from the Variant visualization tool

You can add variants to a case from the **Variant visualization tool**. Use this flow to adjust or combine calls with coordinates from the region currently in view.

Currently supported variant types include **SNV/indel, CNV, UPD, LOH/ROH, and STR**. SV support is planned for future releases.

When reviewing a case, to show only variants entered outside the automated pipeline, apply the [**Manually added variants**](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/quick-filters/user_filters.md#evidence) filter.

{% hint style="info" %}
You can also add a variant from the **Analysis Tools** **tab**. See [**Adding variants to a case from the Analysis Tools tab**](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/manually_add_variants_to_a_delivered_case.md).
{% endhint %}

***

## Adding a variant to a case from the Variant visualization tool

**Prerequisite:** You need the relevant [permissions](/emedgene/emedgene-analyze-manual/settings/user_roles/iam-scopes-emedgene-roles.md).

{% stepper %}
{% step %}
In the **Variant visualization tool**, select **Add Variant** (<i class="fa-plus-large">:plus-large:</i>) from the top navigation panel.
{% endstep %}

{% step %}
Select a variant type.
{% endstep %}

{% step %}
Enter the details for the selected variant type.

By default, the variant type is CNV, and the genomic coordinates are filled from the region in view.

{% tabs %}
{% tab title="SNV" %}

* **Chromosome**
* **Position**
* **REF**
* **ALT**
* **Zygosity** in analyzed samples

<div data-with-frame="true"><figure><img src="https://4225924541-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F2YO86ZgkG5vXGkBAMT71%2Fuploads%2FHe2tSntB0R1IftVoRPtM%2Fimage.png?alt=media&#x26;token=a40b5b43-b4b4-4fe9-9f53-107a3edba1ba" alt=""><figcaption></figcaption></figure></div>
{% endtab %}

{% tab title="CNV or UPD" %}

* **Chromosome**
* **Position Start**
* **Position End**
* **REF** (v100.40 and earlier). On v100.41 and later, **REF** is set to `N` and is not shown.
* **Type**
  * **CNV**: `DEL` or `DUP`
  * **UPD**: `IUPDMAT` (maternal isodisomy), `IUPDPAT` (paternal isodisomy), `HUPDPAT` (paternal heterodisomy), or `HUPDMAT` (maternal heterodisomy)
* **Zygosity** in analyzed samples
* **Quality** **metrics** (v100.41 and later)
  * **Variant quality**: `HIGH`, `MODERATE`, or `LOW`. Default value is `HIGH`.
  * **CN (copy number)**
  * **Mosaic flag** and **Mosaic fraction**

<div data-with-frame="true"><figure><img src="https://4225924541-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F2YO86ZgkG5vXGkBAMT71%2Fuploads%2FeyVnTYy5C5VCErXB0sh6%2Fimage.png?alt=media&#x26;token=39158b8a-4f80-4c6d-ad0a-3d59f7ec5a11" alt=""><figcaption></figcaption></figure></div>
{% endtab %}

{% tab title="LOH/ROH" %}

* **Chromosome**
* **Position Start**
* **Position End**
* **REF** (v100.40 and earlier). On v100.41 and later, **REF** is set to `N` and is not shown.
* **Zygosity** in analyzed samples
* **Quality** **metrics** (v100.41 and later)
  * **Variant quality**: `HIGH`, `MODERATE`, or `LOW`. Default value is `HIGH`.
  * **CN (copy number)**
  * **Mosaic flag** and **Mosaic fraction**

<div data-with-frame="true"><figure><img src="https://4225924541-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F2YO86ZgkG5vXGkBAMT71%2Fuploads%2FTsYgkAkMLbdfnziQrAoe%2Fimage.png?alt=media&#x26;token=ebf0d3d6-81c5-476f-9afc-0e705e2e64cb" alt=""><figcaption></figcaption></figure></div>
{% endtab %}

{% tab title="STR" %}

* **Chromosome**
* **Position**
* **REF Repeats Number**
* **ALT Repeats Number**
* **Repeats Unit**
* **Zygosity** in analyzed samples

<div data-with-frame="true"><figure><img src="https://4225924541-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F2YO86ZgkG5vXGkBAMT71%2Fuploads%2FvvjAsWtOAIWYAHKFXLuR%2Fimage.png?alt=media&#x26;token=e973fa7a-b525-46d6-b9e8-7e2f848a674c" alt=""><figcaption></figcaption></figure></div>
{% endtab %}
{% endtabs %}
{% endstep %}

{% step %}
Select **Create Variant**.
{% endstep %}
{% endstepper %}

**Result:**

* The variant is added to the case.
* Variant annotation: see below.

{% columns %}
{% column %}

#### v100.41 and later

On v100.41 and later, manually added variants go through a full annotation pipeline.

Annotation starts, and a notification tells you that it has started. You cannot finalize the case while annotation is in progress.

When annotation finishes and you get a success message, select **Open variant** to open the **Variant page**.

<div align="center"><figure><img src="https://4225924541-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F2YO86ZgkG5vXGkBAMT71%2Fuploads%2F598LtT042xJfKvwaCrsh%2Fcom.png?alt=media&#x26;token=39258d28-87ab-42ad-a740-8652226b0f62" alt=""><figcaption><p>Variant annotation success message.</p></figcaption></figure></div>

{% hint style="info" %}
The latest available pipeline version is used for annotation of variants added to a delivered case, regardless of the pipeline version selected in **Settings**. The pipeline version used for the annotation is recorded in the **Activity**.
{% endhint %}
{% endcolumn %}

{% column %}

#### v100.40 and earlier

On v100.40 and earlier, manually added variants are not annotated and automatic ACMG scoring is not applied.

In the variant table, you cannot sort these variants by columns that depend on annotation, such as **AI Rank**.

{% hint style="warning" %}
STRs added to a case before v100.41 do not show variant length. Use the repeat numbers and the repeat unit.
{% endhint %}
{% endcolumn %}
{% endcolumns %}

## Learn more

<table data-view="cards"><thead><tr><th></th><th></th><th></th></tr></thead><tbody><tr><td><strong>Variant visualization tool</strong></td><td>Review alignments and supporting evidence in genomic context.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool.md">Learn more</a></td></tr><tr><td><strong>Adding variants to a case from the Analysis Tools tab</strong></td><td>Add a variant from the <strong>Analysis Tools</strong> tab, and filter manually added variants in a case.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/manually_add_variants_to_a_delivered_case.md">Learn more</a></td></tr></tbody></table>


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/manually-add-variant-from-igv.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.