prikaz prve stranice dokumenta Provjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka
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master's thesis
Provjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka
Zagreb: University of Zagreb, Faculty of Agriculture, 2019. urn:nbn:hr:204:265858
Glunčić, Tea
University of Zagreb
Faculty of Agriculture
Animal Science

Institutional repository: Repository Faculty of Agriculture University of Zagreb

Cite this document

Glunčić, T. (2019). Provjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka (Master's thesis). Zagreb: University of Zagreb, Faculty of Agriculture. Retrieved from https://urn.nsk.hr/urn:nbn:hr:204:265858

Glunčić, Tea. "Provjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka." Master's thesis, University of Zagreb, Faculty of Agriculture, 2019. https://urn.nsk.hr/urn:nbn:hr:204:265858

Glunčić, Tea. "Provjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka." Master's thesis, University of Zagreb, Faculty of Agriculture, 2019. https://urn.nsk.hr/urn:nbn:hr:204:265858

Glunčić, T. (2019). 'Provjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka', Master's thesis, University of Zagreb, Faculty of Agriculture, accessed 20 December 2024, https://urn.nsk.hr/urn:nbn:hr:204:265858

Glunčić T. Provjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka [Master's thesis]. Zagreb: University of Zagreb, Faculty of Agriculture; 2019 [cited 2024 December 20] Available at: https://urn.nsk.hr/urn:nbn:hr:204:265858

T. Glunčić, "Provjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka", Master's thesis, University of Zagreb, Faculty of Agriculture, Zagreb, 2019. Available at: https://urn.nsk.hr/urn:nbn:hr:204:265858

Metadata
TitleProvjera točnosti određivanja faze haplotipa putem simuliranih genomskih podataka
Title (english)Verefication of haplotype phase accuracy by simulated genomic data
AuthorTea Glunčić
MentorMaja Ferenčaković (mentor)
Committee memberMaja Ferenčaković (predsjednik povjerenstva)
Committee memberVlatka Čubrić Čurik (član povjerenstva)
Committee memberIno Čurik (član povjerenstva)
Committee memberVladimir Brajković (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Agriculture
(Animal Science)
Zagreb
Defense date and country2019-09-30, 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 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.
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 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.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:204:265858
Study programmeTitle: 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 resourceText
File originBorn digital
Access conditionsAccess restricted to students and staff of home institution
Terms of useLicence In copyright icon
Created on2019-11-19 09:57:14