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SeqUIaSCOPE Documentation

IGV

The IGV module provides an embedded genome browser powered by igv.js, allowing read-level validation of flagged variants and fusion breakpoints directly within the application without any external tools.

Opening IGV

The IGV module is not opened directly from the navigation menu. Instead, it is launched from within the Variant Calling or Fusion Genes modules using the IGV dropdown button. Select one or more patients (up to 4) and click Go to IGV — the application navigates to the IGV tab with the appropriate BAM tracks and loci pre-loaded.

Only variants or fusions that have been flagged in the respective module are available for IGV inspection.

IGV requires BAM files. If no BAM files were provided during upload, the IGV dropdown in the analysis modules will not be available.

Reference Genome

The reference genome is handled differently depending on which module the viewer was opened from.

When the IGV module is opened from the somatic or germline variant calling module, a genome selector is always shown before the viewer loads, so you can choose the reference for the variant tracks. The available options are GRCh38/hg38, hg38 1kg/GATK, GRCh37/hg19, T2T CHM13-v2.0/hs1, and a custom genome configured via reference_paths.json (see Configuration).

When the IGV module is opened from the fusion gene module, the viewer reuses the genome chosen during upload in Step 1, so it matches the reference used for the fusion snapshots. If Don’t create IGV snapshots was selected during upload, the same genome selector is shown in the module before the viewer loads. —

Bookmarks Table

Above the IGV viewer, a bookmarks table lists all flagged variants or fusions for the selected patients. Clicking any row in the table navigates the IGV viewer directly to the genomic position of that variant or fusion breakpoint. For fusions, both breakpoint positions are shown and the viewer jumps to a split view of both loci simultaneously.

Loading and Reloading

Click Load IGV Viewer to initialise the browser with the current tracks and locus. If you change the patient selection after IGV has already been loaded, a dialog will ask whether you want to reload the viewer with the new patient data or continue with the current view.

IGV.js is a web-based implementation of the IGV desktop application. While it covers the essential functionality needed for read-level validation, some advanced features of the desktop version are not available.