Click the "Quick View" button to view a variant image. Sample names with '-trio' at the end will include
paternal,
maternal, and sample info in the image.
Use left/right arrow keys to navigate between rows.
Click Chrom, Region, Sample, Copy Number, Family ID, Paternal ID, Maternal Id, Sex, or Phenotype values
to filter.
Click the View Trio button to view only a trio of samples (Paternal,
Maternal, and Sample) together. Consider combining with the Region filter.
Use the filter button for advanced filtering.
To view BAM files in IGV.js (in-browser):
For local Paraviewer sessions (on your local computer): Click IGV button and select the project directory - you'll see a
warning but files will not be uploaded to a remote location.
For remote Paraviewer sessions (on a server): Click IGV
button to open directly in browser.
IGV Session download options:
Click IGV button to download XML session file, then right-click
and choose click Save Page As.
Click BAM/BAI buttons to download alignment files - these must
be stored in the same location as the corresponding IGV session file.
IGV Session download options for trios: Download the BAM/BAI files from the three trio members and the
IGV session file from the '-trio' row.
Special Info fields provide annotation insights specific to regions when the mouse hovers over the
record row. For example:
SMN Special Info includes the SMN1 and SMN2 copy number.
HBA Special Info includes a sample genotype call, where possible.
Many regions show possible pathogenic vars in each named haplotype - these may appear in the
gene or pseudogene.