Visualization section
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The Visualization section features an IGV-based tool for the visual review of alignment data for validation and interpretation of variant calls.
Drag visualization tracks, set parameters on the right-hand side and zoom in or out to easily customize your view. To see more details, click on the track of interest.
FASTA track displays reference genome sequence;
RefSeq Genes track displays gene(s) and transcript(s) affected by the variant;
Protein domain track (37.0+) - Immediately under the RefSeq track we have added a Protein domain visualization track, using data from Uniprot GRCh38 with a liftover to GRCh37. Clicking a domain will display Name, start, end, ID and link out to UniProt. The track is available for cases created with knowledge graph 73+ versions.
Test Subject VCF track (2.28+) represents proband's variants stored in the VCF file. It may come in handy when you're looking for MNVs or large CNVs that may overlap with other variants;
Test Subject track showcases read mapping (in a FASTQ case or a VCF case with enabled read alignment view).
BAM tracks for non-proband samples represent read alignment in patient's relatives;
BigWig (2.29+)/ TNS (32.0+) track visualizes output of a systematic noise reducing pipeline - tangent normalized signal (TNS). The TNS track simplifies and increases reliability of CNV analysis. Note: On versions prior to 34.0, BigWig / TNS track is only available for WGS cases run from FASTQ.
BAF (32.0+) track presents B-Allele Frequency. The track aids in CNV and LOH analysis. Note: On versions prior to 34.0, BAF track is only available for WES and WGS samples run from FASTQ.
ROH (32.0+) track displays runs of homozygosity from whole genome calls on autosomal human chromosomes. The Regions of Homozygosity (ROH) plot is a visualization of homozygosity that may suggest the presence of uniparental isodisomy or partial isodisomy. Multiple ROH in an individual sample can indicate parental relatedness, which may be associated with an increased risk for a recessive disease. Note: On versions prior to 34.0, ROH track is only available for WGS cases run from FASTQ.
When hovering over the region, the ROH score, the number of homozygous SNVs, the number of heterozygous SNVs, and region's start and end positions are displayed.
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ClinVar* track shows short variants submitted to ClinVar.
ClinVarSV* track shows structural variants submitted to ClinVar.
Curate* track (34.0+)shows short variants that have an entry in the Curate database.
CurateSV* (34.0+) track shows structural variants that have an entry in the Curate database.
*Colors indicate variant pathogenicity:
Green = Benign/Likely Benign,
Yellow = VUS,
Red = Pathogenic/Likely Pathogenic,
Black = Conflicting interpretation of pathogenicity;
Grey = No assertion provided.
To assist in identifying and tracking genomic variants, the platform highlights variant regions with a light blue overlay in all relevant tracks. The highlight remains visible when zooming or panning and dynamically moves to newly selected variants.
To enhance clarity and facilitate a better understanding of genomic data, distinct reference lines are incorporated across various tracks, tailored to provide critical data points at a glance:
TNS Track:
Grey dashed line at Y=0.0
Red dashed line at Y=-0.5
Blue dashed line at Y=0.5
Y-axis fixed range from 2.0 to -2.0
BAF Track:
Grey dashed lines at Y=1.0, Y=0.5, and Y=0.0
Y-axis fixed range from 1.1 to -0.1
LogR (Array Only) Track:
Grey dashed line at Y=0.0
Red dashed line at Y=-0.5
Blue dashed line at Y=0.5
Y-axis fixed range from 2.0 to -2.0
On versions 2.29+, the Visualization section offers two viewing modes: Simple and Advanced.
By default, the Simple mode displays:
RefSeq Genes track;
Test Subject track;
Test Subject VCF track (2.28+).
Additionally, you can select whether to show:
Read alignment tracks for other case samples
(separate feature up to 2.28, part of Additional tracks in 2.29+);
All Curated data tracks for all case samples (2.29+);
All Additional tracks for all case samples (2.29+).
In the Advanced mode, you have more control over track visualization, namely, you can specifically select which Curated data tracks and Additional tracks you want to review for each sample.
Starting from version 38, you can add a variant to a case directly from IGV. Simply click the "Add Variant" button located at the top right of the visualization card. This opens a popup window where you can enter the variant details. By default, the variant type is set to CNV, and the chromosome and coordinates are pre-filled based on the region currently in view. To adjust the span of the suggested coordinates, zoom in or out in IGV accordingly. You can always modify the variant type and genomic coordinates within the popup.
