Named Allele Matcher 201

This document is mainly for those interested in defining your own named allele definitions and covers some of the more advanced details of the Named Allele Matcher .

Scoring

The score for a given named allele is determined by the number of positions at which alleles have been provided.

Example:

	rs1	rs2	rs3	rs4	rs5	score
*1	C	C	T	G	A	5
*2	T	T		A		3

The default named allele definitions are designed to assume that missing alleles are the same as the reference named allele, which is defined as the first named allele in the definition file.

It is, however, possible to increase the score of a named allele by specifying the reference allele. For example, this gene definition table is effectively identical to the one above, but *2 has a different score.

	rs1	rs2	rs3	rs4	rs5	score
*1	C	C	T	G	A	5
*2	T	T	T	A	A	5

Exemptions

src/main/resources/org/pharmgkb/pharmcat/definition/alleles/exemptions.json gives you a way to modify the behavior of the Named Allele Matcher.

Ignoring Named Alleles

If you are designing your own named allele definitions, you might need to define a named allele but not want it to be considered by the Named Allele Matcher.

You can add an exemption for this using ignoredAlleles and ignoredAllelesLc (the latter is just a lower-cased collection of the former).

  {
    "gene": "XXX",
    "ignoredAlleles": [
      "*1S"
    ],
    "ignoredAllelesLc": [
      "*1s"
    ]
  }