> 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_setup/enabling_visualization_for_a_vcf_case.md).

# Enabling visualization for a VCF case

**Loading local alignment files to your case in Emedgene.**

Visualization is automatically available for cases analyzed from **FASTQ** or **BAM** files. For cases analyzed only from **VCF files**, read alignment visualization can still be enabled by providing **alignment files** (BAM+BAI or CRAM+CRAI).

You can enable mapping visualization for a VCF case in three ways:

* **API-based case creation:** Define the location of alignment files directly in the JSON payload.
* **Batch upload:** Include the paths to visualization files in the input CSV when uploading cases in bulk.
* **Manual upload of local alignment files:**

1. Click the Load local file button on top of the Visualization section.
2. Select relevant alignment files stored on your PC.
3. Once uploaded, choose which samples to visualize by selecting their names from the top of the viewer.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-e90a4e9a5583fe107cb99df518d4a1ede22514ad%2Fenabling_visualization_for_a_vcf_case_1_image.png?alt=media)


---

# 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_setup/enabling_visualization_for_a_vcf_case.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.