Visualization tracks

Default tracks

1. FASTA track displays reference genome sequence.

1. RefSeq Genes track displays gene(s) and transcript(s) affected by the variant.

1. Protein domain track uses data from Uniprot GRCh38 with a liftover to GRCh37.

   Clicking a domain visual opens an information window that displays the protein domain name, start and end positions, domain ID, and a link to UniProt. The track is available for cases created with knowledge graph 73+ versions.

1. Test Subject VCF track 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. When you click a variant position on the proband VCF track, a popup appears displaying detailed information about the selected variant.

1. Test Subject track showcases the BAM/CRAM read mapping (in a FASTQ case or a VCF case with enabled read alignment view).

Curated data tracks

1. ClinVar track shows short variants submitted to ClinVar.

1. ClinVarSV track shows structural variants submitted to ClinVar.

1. Curate track shows short variants that have an entry in the Curate database. Clicking a variant in the Curate track opens an information window displaying the following details:

   • Variant ID: Clickable link that opens the variant’s Curate page in a new tab

   • Variant type

   • Main effect

   • Chromosome and position/range

   • Transcript (if available)

   • Gene-related disease

   • Pathogenicity

1. CurateSV track shows structural variants that have an entry in the Curate database.

Knowledge bases tracks

1. OMIM track displays genes linked to known genetic disorders, providing curated insights into disease associations, inheritance patterns, and direct access to OMIM entries for deeper clinical context.

2. ClinGen track highlights genes or regions with clinically reviewed dosage sensitivity scores, color-coded by evidence level, to support interpretation of pathogenicity and genomic stability.

Population data tracks

1. Historic and Historic SV tracks displays historically annotated SNVs and SVs from organizational defined databases, providing insights into allele frequency and zygosity counts (Het, Hom, Hemi) and list of recent samples for contextual interpretation. Track names are equal to the organizational database names defined in settings.

2. gnomAD SV track displays structural variants from the gnomAD database, providing population-level insights into variant frequency and distribution across diverse cohorts to support clinical relevance assessment.

3. DGV Gold track displays high-confidence structural variants curated by the Database of Genomic Variants, offering a reference for common benign variants to aid in distinguishing pathogenic findings.

4. Decipher Healthy Population track displays variants observed in healthy individuals from the Deciphering Developmental Disorders study, helping assess variant pathogenicity by comparing against a baseline of unaffected genomes.

Additional tracks

1. BAM tracks for non-proband samples represent read alignment in patient's relatives.

1. BigWig TNS track represents copy number signal after tangent normalization, allowing clearer visualization of copy number variations by reducing noise and technical bias. The track is available for cases that include a BigWig.tns file.

1. BAF track presents B-Allele Frequency. This track reveals allelic imbalance across the genome, helping detect events like LOH or copy number alterations by showing the proportion of reads supporting the alternate allele. The track is available for cases that include a BAF.bedgraph file.

1. ROH 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. 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. The track is available for cases that include an roh.bed file.

1. SV VCF track displays structural variants from the input VCF file when applicable. It is designed to visualize variants that may be filtered out by the EMG pipeline and not shown by default, including breakends, translocations, and inversions.

2. Log R track visualizes the log ratio of observed probe intensity to expected intensity across the genome. This helps identify regions where the DNA copy number may be increased (duplication) or decreased (deletion). The track is available for cases that include an lrr.bedgraph file.

3. Target count track represents raw sequencing depth for target regions before any signal normalization.

   The track is available for cases that include a .target.counts.bw file.