PSIKO2: a fast and versatile tool to infer population stratification on various levels in GWAS

Andrei-Alin Popescu, Katharina Huber

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Genome-Wide Association Studies are an invaluable tool for identifying genotypic loci linked with agriculturally important traits or certain diseases. The signal on which such studies rely upon can however be obscured by population stratification making it necessary to account for it in some way. Population stratification is dependent on when admixture happend and thus can occur at various levels. To aid in its inference at the genome-level, we recently introduced PSIKO and comparison with leading methods indicate that it has attractive properties. However uptil now it could not be used for local ancestry inference (LAI) which is preferable in cases of recent admixture as the genome level tends to be too coarse to properly account for processes acting on small segments of a genome.To also bring the powerful ideas underpinning PSIKO to bear in such studies, we extended it to PSIKO2 which we introduce here.

Availability: Source code, binaries, and user manual are freely available at
Original languageEnglish
Pages (from-to)3552-3554
Number of pages13
Issue number21
Early online date2 Jul 2015
Publication statusPublished - 1 Nov 2015


  • Q-matrix
  • population stratification
  • Local Ancestry Inference
  • GWAS
  • Genome-Wide Association Studies

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