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  A method for single nucleotide polymorphism calling in diploid individuals

Weckeck, L. (2017). A method for single nucleotide polymorphism calling in diploid individuals. Master Thesis, Universität zu Lübeck, Institut für Neuro- und Bioinformatik, Lübeck.

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Genre: Thesis
Other : Ein Verfahren zur Identifikation vo Einzelnukleotid-Polymorphismen in diploiden Individen

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Weckeck_Lennart_master_2017.pdf (Publisher version), 747KB
 
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Weckeck, Lennart, Author
Haubold, Bernhard1, Referee           
Affiliations:
1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644              

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 Abstract: In this thesis, an approach to calling single nucleotide polymorphisms (SNPs)
in genomes of diploid individuals is developed based on estimations of the global per-base
error rate and heterozygosity. This new method is implemented along with an alternative
calling strategy based on per-site base error rates. The implemented procedures are evaluated
on simulated sequencing data and real sequencing data of inbred mice, and compared
with established SNP calling tools. While the newly developed method works well on simulated
data, the results on real data do not match those of the established tools. According
to population genetic theory, inbred mouse genomes should be completely homozygous,
which is, however, not the case. The hypothesis that SNPs in inbred mice are located in
critical genes, is investigated, because mutations at these sites are potentially lethal. The
Overrepresentation Enrichment Analysis performed on sequencing data of inbred mouse
strain C57BL/6NJ shows some support for the hypothesis, but remains inconclusive.

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Language(s): eng - English
 Dates: 2017-12-132017-12-13
 Publication Status: Issued
 Pages: 47
 Publishing info: Lübeck : Universität zu Lübeck, Institut für Neuro- und Bioinformatik
 Table of Contents: Contents
1 Introduction 1
1.1 Related Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2 Methods for SNP calling in diploid genomes 5
2.1 Basic concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2 Maximum likelihood estimation of heterozygosity and error rate . . . . . . . 7
2.3 The global method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.4 The local method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.5 Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.6 Reference tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3 Empirical results on simulated data 17
3.1 Data generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.2 Analysis methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.3.1 Sid priors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
3.3.2 Sid parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
3.3.3 Comparison of Sid with SAMtools and GATK . . . . . . . . . . . . 22
3.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
4 Empirical results on real data 25
4.1 Data generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4.2 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
4.2.1 Comparison of reference tools . . . . . . . . . . . . . . . . . . . . . . 27
4.2.2 Evaluation of Sid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
4.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
5 Analysis of mouse data 33
5.1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
5.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
5.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
5.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
6 Conclusion 43
6.1 Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
 Rev. Type: -
 Identifiers: Other: Dipl/12911
 Degree: Master

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