# Visual mode

Pushing the VISUAL button (available in ANALYSIS mode only) in the side bar opens the VISUAL mode:


This mode features an integrated version (opens new window) (v2.5.4) of Integrative Genomics Viewer (IGV) (opens new window):

With IGV, you can visualize all variants in an analysis, along with customisable tracks at three different levels: global, user group or analysis.

# Global tracks

Global tracks are available to all users. These currently include:

  • REFGENE: Transcripts from RefGene.
  • GENE PANEL: Regions covered by the current gene panel.
  • VARIANTS: All variants in the same sample (analysis) after filtering.
  • CLASSIFICATIONS: All existing classifications present in the database.

# Your tracks (user group)

Your tracks are specific to your user group in ELLA. These typically include data from external sources and references.

# Analysis tracks

Analysis tracks are specific to the analysis (depending on configuration). These may include:

  • BAM files: Raw alignments (HTS data only), split by family members if relevant
  • VCF: All variants called in the VCF file (HTS data only, within gene panel, no filtering)
  • CNV: Called CNVs (HTS data only)

# Mark as TECHNICAL

A button T is available in the side bar next to each variant for quickly marking technical variants. This works the same as in Quick classification mode, where clicking the button moves the variant to the TECHNICAL VARIANTS section in the side bar. If applicable, add a comment before moving to the next variant; this will also be reflected in the ANALYSIS SPECIFIC comment field on the CLASSIFICATION page.

Last Updated: 12/18/2020, 10:03:27 PM