> 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.md).

# Variant visualization setup

**Variant visualization setup** covers configuration before and during case review: enabling read alignment for VCF cases and connecting Emedgene to desktop IGV for extended mapping review.

## Learn more

<table data-view="cards"><thead><tr><th></th><th></th><th></th></tr></thead><tbody><tr><td><strong>Enabling visualization for a VCF case</strong></td><td>Provide BAM+BAI or CRAM+CRAI alignment files so read alignment appears in the <strong>Variant visualization tool</strong>.</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_setup/enabling_visualization_for_a_vcf_case.md">Learn more</a></td></tr><tr><td><strong>Integration between Emedgene and desktop IGV</strong></td><td>Enable desktop IGV to follow the genomic position of the variant you select in <strong>Emedgene</strong>.</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_setup/integration_between_emedgene_and_desktop_igv.md">Learn more</a></td></tr><tr><td><strong>Loading alignment files to your desktop IGV</strong></td><td>Send BAM/CRAM alignment files from <strong>Emedgene</strong> to desktop IGV.</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_setup/loading_alignment_files_to_your_desktop_igv_-320+.md">Learn more</a></td></tr><tr><td><strong>Variant visualization</strong></td><td>Review alignment, annotation, and population data 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.md">Learn more</a></td></tr></tbody></table>


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