Provjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka

master's thesis

• Title (english): Verefication of haplotype phase accuracy by simulated genomic data
• Author: Tea Glunčić
• Mentor: Maja Ferenčaković (mentor)
• Committee member: Maja Ferenčaković (predsjednik povjerenstva)
• Committee member: Vlatka Čubrić Čurik (član povjerenstva)
• Committee member: Ino Čurik (član povjerenstva)
• Committee member: Vladimir Brajković (član povjerenstva)
• Granter: University of Zagreb; Faculty of Agriculture; (Animal Science); Zagreb
• Defense date and country: 2019-09-30, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Agronomy

Abstract

Imputacija genotipa je termin koji se koristi za opisivanje procesa predviđanja ili umetanja genotipa koji nisu testirani na uzorku pojedinca. To se često koristi za imputaciju cijelokupnog genoma. U radu je ispitano točnost procjenjivanja imputacije. Podaci su simulirani u programskom paketu QMSim. Simulirane su dvije populacije sa 2000 životinja i sa 500 životinja. Kako bi mogli dobro ispitati imputaciju moralo se staviti nedostajući genotipovi. To je rađeno uz pomoć SAS paketa i uz proceduru... More SURVEYSELECT. Time su dobivena 4 slučaja. Napravljeno je da nedostaju 1500 SNP-ova i 500 SNP-ova. Imputacija je napravljena u programskom paketu AlphaImpute. On može imputaciju vršiti na dva načina. Uz pomoć pedigrea i HMM. Na kraju je dobiveno osam scenarija u kojima se ispitivala točnost imputacije na temelju koliko je SNP-ova imputirano i ovisno o tome na koji model je imputiranje izvršeno. Less

Abstract (english)

Genotype imputation is the ultimate used to describe the process of predicting or inserting genotypes that have not been tested on an individual sample. It is often used to impute the entire genome. The accuracy of imputation estimation is examined in the paper. The data were simulated in the QMSim software package. Two populations with 2000 animals and 500 animals were simulated. To be able to test the imputation accuracy they missing genotypes had to be inserted. That was done using the SAS... More package and procedure SURVEYSELECT. With this we got 4 cases. 1500 SNPs and 500 SNPs were missing. Imputation was made in the AlphaImpute software package. There are two ways to perform imputation. With the help of pedigree and HMM. Finally, 8 scenarios were obtained in which the imputation accuracy test was performed based on how many SNPs were imputed and depending on which model the imputation was performed. Less

• Keywords: imputacija; QMSim; AlphaImpute; HMM
• Keywords (english): imputation; QMSim; AlphaImpute; HMM
• Language: croatian
• URN:NBN: urn:nbn:hr:204:265858
• Study programme: Title: Animal Genetics and Breeding; Study programme type: university; Study level: graduate; Academic / professional title: magistar/ magistra inženjer/inženjerka genetike i oplemenjivanja životinja (magistar/ magistra inženjer/inženjerka genetike i oplemenjivanja životinja)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2019-11-19 09:57:14