Default tracks

These visualization tracks provide the core genomic context for variant review and cannot be hidden from the view in Track Manager.

FASTA

The FASTA track displays the reference genome sequence.

FASTA track

RefSeq Genes

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

RefSeq Genes track

Protein domain

The Protein domain track uses data from UniProt GRCh38 with liftover to GRCh37.

Click a domain to open more details:

• Protein domain name

• Start and end positions

• Domain ID

• Link to UniProt

This track is available for cases created with knowledge graph version 73 or later.

Protein domain track

Test Subject VCF

The Test Subject VCF track shows the proband variants stored in the input VCF.

Use it to review nearby variants, including MNVs and large CNVs.

Click a variant position to open a popup with the variant details.

Test Subject VCF track

Test Subject BAM

The Test Subject BAM track shows BAM or CRAM read alignment for the proband. Use this track to review read support for variants in the genomic context of the case.

Starting in v100.40.0, the Test Subject BAM track supports two views:

• Standard view: Shows read alignment without phasing information. This is the default view and matches the Test Subject BAM behavior available before v100.40.0.

• Phased view: Groups reads by haplotype when phased BAM files are available.

In v100.40.0+, for MRJD variants the Test Subject BAM track always opens in phased view.

Standard view

In standard view, the Test Subject BAM track shows read mapping for the proband without grouping reads by haplotype.

Test Subject BAM track in standard view, showing read alignment for the proband.

Prerequisites for standard view

This track is available in:

• FASTQ cases

• VCF cases with read alignment view enabled

Phased view

In phased view, the Test Subject BAM track groups reads by haplotype and colors reads by phase block. Use this view to compare read support across haplotypes.

• Red reads support haplotype 1.

• Blue reads support haplotype 2.

• Gray reads are not phased. The system cannot confidently assign them to haplotype 1 or haplotype 2.

Test Subject BAM track in phased view, showing proband reads grouped by haplotype.

Prerequisites for phased view

To use phased view, upload output from DRAGEN 4.5 or later Germline analysis for Illumina TruPath Genome data with the case VCF. The upload must include one or both of the following file sets:

• Phased BAM and BAI files for phased variants:

  • <sample_name>.bam

  • <sample_name>.bam.bai

• MRJD phased BAM file for phased small variants in paralogous regions called with the DRAGEN Multi-region Joint Detection caller:

  • <sample_name>.mrjd.phased.bam

Switching between views

To switch from standard view to phased view, toggle on Phased next to Test Subject BAM in the Track Manager. To switch back to standard view, toggle off Phased.

Enabling phased view for the Test Subject BAM track.