Integrative Genomics Viewer (IGV)

Load the patient VCF file into IGV.

Load the corresponding BAM file (alignment).

Navigate to the coordinate of the candidate mutation.

Examine read support: check for strand bias and mapping quality (MQ).

Compare against the 'Control' track if available.

Manually confirm or reject the variant for clinical reporting.

Perform whole-genome sequencing on the edited cell line.

Load the resulting alignments into IGV.

Upload a BED file containing predicted off-target coordinates.

Use the 'Group by' feature to organize reads by alignment strand.

Visually inspect for low-frequency insertions or deletions at the predicted sites.

Load RNA-seq BAM files and a Gene Annotation track (GTF).

Right-click the coverage track and select 'Sashimi Plot'.

Filter junction views by minimum read support.

Identify arcs representing novel exon-exon connections.

Export the plot for publication.

Load segment files (.seg) derived from array-CGH or sequencing.

Select 'Heatmap' view for multiple samples.

Sort samples by genomic gain at a specific oncogene locus (e.g., HER2).

Correlate CNV data with clinical metadata using the Attribute viewer.

Load ChIP-Seq or ATAC-Seq BigWig tracks.

Set a uniform data scale across all tracks for fair comparison.

Overlay transcription factor binding sites (BED).

Identify regions of open chromatin coincident with active promoter marks (H3K4me3).

Load long-read BAM files.

Enable 'Color by Tag' to view phasing information (HP tag).

Inspect large insertions or deletions that span thousands of base pairs.

Verify if structural variants are linked on the same haplotype.

Configure data tracks to point to publicly accessible URLs (e.g., Dropbox/S3).

Optimize the view and color-coding.

Save the Session XML.

Email the XML file to a collaborator, who opens it in their IGV instance to see the exact same view.