# IGV
We offer two options to browse the raw data:
- Desktop IGV
- Browser-embedded IGV
You can switch between these two options on the fly by clicking the "Settings" button and selecting your preference.
When you choose the "Desktop App" option, the IGV button will appear on the right. Click on this button to stream the data to your desktop IGV app.
To analyze any location, variant, or target region on the IGV, you can click the 🔍 button. Depending on your selection, this will initiate the IGV without leaving the browser and load the sample BAM, VCF and target regions, or stream the data to your desktop IGV app.
Using the "Browser" option, you can add more samples to compare by using the search field on the upper-left corner.
# DNA Methylation
For PacBio HiFi long-read WGS samples, DNA methylation BED tracks generated by pb-CpG-tools (opens new window) are available, displaying per-site CpG methylation levels across the genome — see Methylation Analysis for details.
In addition to the per-site CpG pileup track, MethBat (opens new window) annotated regions are loaded as a separate BED track in IGV. This track shows region-level methylation values for UCSC CpG island regions, allowing comparison between per-site and per-region methylation data side by side.
# Haplotype Grouping
For long-read WGS samples (PacBio and ONT), reads are displayed with haplotype grouping and coloring based on the HP (haplotype) tag assigned during phasing. This allows visual inspection of allele-specific read support for variants of interest. You can activate or deactivate haplotype grouping and coloring using the checkboxes in the IGV panel.
# Targeted Caller BAM
For analyses that include targeted variant calling, clicking the IGV button on any variant loads the targeted caller BAM alongside the main aligned BAM. This BAM contains haplotype-resolved reads from targeted gene families, enabling visual inspection of individual haplotypes and copy-number resolution in segmental duplication regions. For example, PacBio HiFi long-read WGS samples load the Paraphase BAM (visible in the screenshot above) — see Targeted Variant Calling for details.
If you want to change the default IGV type, click on your "Profile" button on the top-right of the page and go to "User Preferences" under "User and Site Settings" on top-right. Here, you can change your default IGV type.
