Incorrect annotation and visualization of a small minority of overlapping variants

Issue description

An issue relating to identifying overlapping annotations has been identified that has several potential effects, described below. All are expected to be rare.

1) Annotate RNA Variants incorrectly annotates a small number of variants

Using Annotate RNA Variants, a tool delivered by the Biomedical Genomics Analysis plugin, a small number of variants at specific positions of a given mRNA track may have the following annotations incorrectly applied:

• Matches known intron
• Possible splice signatures
• Conserved splice signature

It is the features of a particular mRNA track that influence the locations affected by this problem. The read mapping and reference sequence used do not have any influence.

In affected software versions, this problem is present in the Perform QIAseq Multimodal Analysis (Illumina) and the Perform QIAseq RNA Fusion XP Analysis ready-to-use workflows, as these include the Annotate RNA Variants tool. The preconfigured mRNA track used in these workflows, Homo_sapiens_refseq_GRCh38.p13_no_alt_analysis_set_pt.wonderland_RNA, may have incorrect  annotations for variants called at the following 23 genomic positions:

We cannot exclude the possibility that variants at other positions may be affected, but the above list includes the ones we expect to be affected in this particular mRNA track.

If you use a different mRNA track with this tool, or with workflows that include this tool, then the above position list does not apply. Other positions are likely to be affected. We expect the number of positions to be of the same magnitude.

2) Transcript Discovery occasionally identifies an incorrect exon boundary

Using Transcript Discovery, a tool delivered by the Transcript Discovery plugin, an incorrect exon boundary can occasionally be identified. Due to the expected level of sensitivity and precision of this tool, we expect this to have very little impact in practice.

3) Visualization of affected variant annotations is not as expected

This issue can manifest itself as a cosmetic problem in the rendering of annotations and variants, in some editors. In affected positions, annotations and variants may be displayed in multiple vertical layers, instead of beside one another, or they may appear to be “hopping” vertically when you scroll in the editor.

This is a visualization problem that can affect track views, track lists, and (non-track) sequence editors. The underlying, recorded position of the annotations and variants is not affected.

Affected software and tools

This issue was addressed in CLC Genomics Workbench 20.0.3 and CLC Genomics Server 20.0.3.

• Annotate RNA Variants of the Biomedical Genomics Analysis plugin is affected when used on CLC Genomics Workbench 20.0, 20.0.1 or 20.0.2. The same tool delivered by the Biomedical Genomics Analysis Server Plugin is affected when used on CLC Genomics Server 20.0, 20.0.1 or 20.0.2.
• Transcript Discovery of the Transcript Discovery plugin is affected when run on CLC Genomics Workbench version 20.0.2 or any earlier version. The same tool delivered by the Transcript Discovery Server Plugin is affected when used on CLC Genomics Server 20.0, 20.0.1 or 20.0.2.
• Visualizations of affected results can be affected in CLC Genomics Workbench version 20.0.2 or any earlier version.