TriTyper is software for tri-allelic SNP calling. It is composed of three programs:
  • TriTyper Importer imports raw intensity data and stores this in a binary data format. These files are required by
  • TriTyper Discoverer, which can discover triallelic SNPs based on raw intensity data, and
  • TriTyper Imputer, which uses LD information for 1,204 triallelic SNPs to infer triallelic genotypes, if only biallelic genotype calls are available.
If you want to become familiar with TriTyper, it is recommended you download the example data (47 samples, typed for 317,503 SNPs using Illumina HumanHap300 arrays). Once you have extracted this Zip file you can familiarize yourself with the data formats we have used. Additionally, you can use these files to assess how importing works and how triallelic SNP discovery and imputation perform.


Franke L, de Kovel CG, Aulchenko YS, Trynka G, Zhernakova A, Hunt KA, Blauw HM, van den Berg LH, Ophoff R, Deloukas P, van Heel DA, Wijmenga C. Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. Am J Hum Genet. 2008. 82:1316-33. Free PMC article

Trityper website