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Filippo Biscarini edited this page Jul 4, 2016 · 2 revisions

Welcome to the RoHet wiki!

The project is to develop tools for the analysis of runs of heterozygosity. This is motivated (besides intellectual and scientific curiosity) by the following two sub-projects:

  1. within Methagene/Climgen: work has been done on proposing ROHom for association studies (aside GWAS and resampled predictive models); ROHet may be useful to track signatures of negative or balancing selection

  2. collaboration with the University of Aalborg: study of introgression, hypervariable regions etc. on data from rare Danish cattle breeds, pig breeds and wild boars, dog breeds ...

  3. possible use also in Fecund (cooperation with P. Ajmone, Marcello & Mario)

Methods

Two main approaches:

  1. consecutive ROHhet/ROHom (as in Marras et al. / as implemented in Zanardi)
  2. sliding-window approach (as in Plink)

Software

  • From Zanardi: Python functions for consecutive ROHet/ROHom
  • R package: R code (to be written) for ROHet (maybe also ROHom) with a sliding-window approach (simil-Plink)

At a later stage, both methods will probably be implemented both in Python and R

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