> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/annotation/core-functionality/junction-preserving.md).

# Junction Preserving Annotation

### Background

When a variant can be moved (due to alignment) across junctions (e.g. start, stop or splice site), the annotation may vary depending on which exact alignment was used. For example, a left-aligned deletion that effects the splice acceptor site, upon right-alignment, may become an exon variant.

![Deletion at exon boundary](/files/FBICViOxmsL6GI9oQbA4)

Note that:

* When right-aligned the variant starts at the first base of the exon (as pictured).
* When left-aligned the variant can be shifted two base pairs and starts at a splice acceptor site.

From the point of view of the translation mechinary, the important question is whether the sequence that identifies a junction is preserved, regardless of the variant position. In the case of the deletion above, we believe that the variant is more accurately characterized as an `inframe_deletion` not a `splice_acceptor_variant` as splice acceptor sequence `AG` is unaffected.

When faced with such variants, we will assign junction disrupting consequnces only if the variant cannot be shifted out of the junction.

### Implementation

By default and convention, the left-aligned variant is annotated. If the variant overlaps a junction (as judged by consequences), it is right-aligned and annotated. If both alignment produces junction disruption, the left-aligned annotation is reported. If however, only one of the alignment causes junction disruption but not the other, the non-junction-disrupting annotation is reported.

{% hint style="info" %}
This only effects transcript annotations. Supplementary annotations are reported on the left-aligned variant and HGVS notations are calculated on right-aligned variant.
{% endhint %}


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