Additional tracks

Optional alignment, signal, and structural tracks in the variant visualization tool.

These tracks appear when supporting files are available for the case.

BAM

BAM tracks for non-proband samples show read alignment in relatives.

BAM track showing read alignment for a non-proband sample.

When loading BAM/CRAM tracks from BaseSpace storage, make sure the matching BAI/CRAI index files have BaseSpace identifier numbers that are close.

If the identifiers are far apart, the visualization may fail to load due to file lookup limitations in BaseSpace.

BigWig TNS

The BigWig TNS track shows copy number signal after tangent normalization.

Use it to review copy number changes with reduced noise and technical bias.

This track is available for cases that include a BigWig.tns file.

BigWig TNS track showing normalized copy number signal.

BAF

The BAF track shows B-Allele Frequency. This track reveals allelic imbalance across the genome by showing the proportion of reads supporting the alternate allele.

Use it to detect events like LOH or copy number alterations.

This track is available for cases that include a BAF.bedgraph file.

BAF track showing B-Allele Frequency across the region.

ROH

The ROH track shows runs of homozygosity on autosomal human chromosomes from whole-genome calls.

Use it to review homozygosity patterns that may suggest 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.

Hover over a region to see:

• ROH score

• Number of homozygous SNVs

• Number of heterozygous SNVs

• Start and end positions

This track is available for cases that include an roh.bed file.

ROH track showing a run of homozygosity region.

SV VCF

The SV VCF track shows structural variants from the input VCF when applicable.

Use it to visualize variants that may be filtered out by the Emedgene pipeline, including breakends, translocations, and inversions.

Log R

The Log R track shows the log ratio of observed probe intensity to expected intensity across the genome.

Use it to identify regions with increased (duplication) or decreased (deletion) DNA copy number.

This track is available for cases that include an lrr.bedgraph file.

Target count

The Target count track shows raw sequencing depth for target regions before signal normalization.

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