Naming Example

4. GS Amplicon Variant Analyzer – Special Topics : 4.2 Intelligent Variant Naming : 4.2.5 Naming Example

4.2.5

Table 4‑3 shows how 4 different but related Variant Patterns end up being named by the naming scheme, showing an example of each Tier.

Final Naming Tier	Variant Pattern	Final Name
Tier 1	d(327)m(339-342)	327:A/-,339-342:AAGC/AAGC
Tier 2	d(327)m(339-343)	327:DEL,339-343:REF(5)
Tier 3	d(327-328)m(339-343)	d(327-328)m(339-343)
Tier 4	d(327-328)m(339-343)m(347)	Var_16

Table 4‑3: Example final Variant names that could be used, for each of the 4 tiers schemes, using a set of Variant patterns of increasing complexity. See text below for more details.

The Tier 1 example shows that the Variant pattern can be expressed as a name exactly 25 characters in length. Since this meets the length constraint, the Tier 1 name is used as this Variant’s final name.

In the Tier 2 example, the Variant pattern from the Tier 1 example has been altered to extend the match range by an extra base. If this pattern were converted into a Tier 1 name, it would read: “327:A/-,339-343:AAGCA/AAGCA” (assuming base 343 of the Reference Sequence were an A). This name exceeds the 25 character limit by two characters, so the software rejects it and constructs a Tier 2 name. The Tier 2 final name, “327:DEL,339-343:REF(5)”, has 22 characters, so it is adopted as the final name for this Variant.

The Tier 3 example Variant pattern is the same as the Tier 2 pattern except that it has an extra base in its deletion. If this pattern were expressed as a Tier 2 name, it would read: “327-328:DEL,339-343:REF(5)”. This name has 26 characters so the software rejects it and constructs a Tier 3 name, using the Variant Definition Syntax: “d(327-328)m(339-343)”. Since the Tier 3 name is only 20 characters it is adopted as the final name for the Variant.

In the Tier 4 example, the Variant pattern from the Tier 3 example is altered by the addition of an extra match constraint. Since Tier 3 names are the same as the Variant Pattern, and the pattern here already exceeds 25 characters (see Table 4‑3), the software resorts to the final tier, and the generic “Var_16” is used as the final name.