Annotate from Known Variants compares variants in an input track to known variants provided in another track. The tool outputs a new track containing the original variants with information added where matching known variants were identified.
To run the Annotate from Known Variants tool, go to:
Toolbox | Resequencing Analysis () | Variant Annotation () | Annotate from Known Variants ()
There are three levels of matches between variants in the input track and the known variants track:
- Exact match Exact matches are those variants where the position and allele are identical in the input and known variants tracks. For exact matches, the output track includes information about that variant taken from the known variants track.
- Partial MNV match Partial MNV matches are those where the variant in the input track consists of an SNV or an MNV that has an allele sequence that is contained within the allele sequence of an MNV in the known variant track. These are not exact matches due to a difference in the variant lengths. Information from known variants are not transferred for partial matches.
- Overlap Where a variant in the input track overlaps a variant in the known variants track, but is not categorized as an exact match or a partial MNV match, it will be documented as an Overlap. Information from known variants are not transferred for overlap matches.