Milí kolegové a kolegyně,
chtěli bychom vás srdečně pozvat na další přednášku semináře, která se koná již zítra, tj. ve středu 20.12.2017, od 17:20 v posluchárně S4.
Hostem na semináři bude Tomáš Gavenčiak z MFF UK a téma přednášky bude
Genotype refinement with PBWT
Těšíme se srdečně na vaši účast!
Za všechny organizátory semináře s pozdravem, Petr Daněček
Stránky semináře http://bioinformatika.mff.cuni.cz/seminar/
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Tomáš Gavenčiak
Genotype refinement with PBWT
Genotype refinement is one of the latest phases of the genome sequencing process. It is used to infer the most likely genotype from the observed genotype likelihoods and is usually followed by variant phasing. Most of the state-of-the-art approaches for these steps use population data as a reference, modeling recombinations and population inheritance using the Li-Stephens model. The problems are usually stated as Hidden Markov Models. However, direct computation of these HMMs is very costly and faster methods are needed.
After a brief introduction to the field and the Li-Stephens model, I will introduce some algorithms based on PBWT used to accelerate the computation. I will described the Hap-hedge structure which was developed by the Eagle2 phasing software and show a modified approach which can be extended to the problem of genotype refinement, which is the main subject of my current work.