Variants are classified into four different types:
- A single nucleotide variant. This means that one base is replaced by one other base. This is also often referred to as a SNP. SNV is preferred over SNP because the latter includes an extra layer of interpretation about variants in a population. This means that an SNV could potentially be a SNP but this cannot be determined at the point where the variant is detected in a single sample.
- This refers to the event where one or more bases are inserted in the experimental data compared to the reference.
- This refers to the event where one or more bases are deleted from the experimental data compared to the reference.
- This is a more complex event where one or more bases have been replaced by one or more bases. Basically, this type represents variants that cannot be represented in the other three categories. An example could be
AAA->CC. This cannot be resolved into a set of SNVs because the number of bases is different between the experimental data and the reference, it is not an insertion because something is also deleted from the reference, and it is not a deletion because something is also inserted.
The relationship between adjacent variants is governed by the concept of a linkage group (see Linking adjacent variants in linkage groups