Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 10 of 10 for “"GATK"”.
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Cancer risk prediction with next generation sequencing data using machine learning
… as well as with Genome Analyzer Tool Kit (GATK). Subsequently, the variants are encoded and feature selection is performed with the Pearson correlation coefficient (PCC) and the chi-square 2-df statistical test. Finally, 90:10 cross validation is performed by applying the support vector …
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Investigation of heterozygousity of yeast plasmid
… methods used during this research, including the GATK software used to sequence the plasmid genome. An extensive table of results was made, listing the strain name, if the strain was found to be heterozygous or homozygous and how many heterozygousities were found. The thesis also compared the …
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Data-Intensive Biocomputing in the Cloud
… variant pipeline called genome analysis toolkit (GATK), on the Windows Azure HDInsight cloud platform. Together with a parallel implementation of GATK on Hadoop, we evaluate the potential of using cloud computing for large-scale DNA analysis and present a detailed study on efficiently utilizing …
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Bioinformatics Analysis of Whole-Exome Sequencing Data for the Identification of Nuclear and Chloroplast Diversity in Barley
… calling pipelines, Bowtie2/FreeBayes and BWA/GATK, a small subset of samples was used and variants identified and validated against an independent set of iSelect SNP-chip data which showed higher accuracy for BWA/GATK. I subsequently used the latter for the rest of this …
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Empirical accuracy bounds for next-generation sequencing variant calling workflows
… datasets to showcase how the behavior of BWA and GATK workflows changes as a function of read lengths, error rates, quality scores, error types, and mutation types. We utilize these results to quantify the performance gains that can be expected by altering these properties of an NGS dataset. Our …
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A new filtering method for improving the quality of variant discovery
… and when sequencing pipelines other than GATK are used. Finally, since the training needs to be performed only once, there is a significant saving in running time when compared to VQSR (4 versus 50 minutes approximately for filtering the SNPs of a WGS Human sample).
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Genome-graph based genotyping with applications to highly variable genes in P. falciparum
… to single-reference based approaches (GATK), before uncovering new biology. Expressing each diverged DB haplotype as a mosaic of the others, I find widespread recombination in each gene, and also discover recent evidence of gene conversion between the two genes. In summary, this thesis …
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Identification of Familial Wilms Tumor Predisposition Genes Using Whole Genome Sequencing
… cancer. Variant calling was performed by GATK, FamSeq and CASAVA to detect single nucleotide variations (SNVs), insertions/deletions (indels) and structural variants. Shared variants within each family were identified and prioritized based on expression in fetal kidney, minor allele …
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Genetic diversity and population structure within Botswana: association with HIV-1 infection
… was performed using Genome Analysis Tool Kit (GATK) and BCFTools. Variant characterisation was achieved by annotating the variants with a suite of databases in ANNOVAR. The genomic architecture of Botswana was assessed through principal component analysis and structure analysis and FST. …
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Whole exome sequencing to investigate genetic variants of non-syndromic hearing impairment in a population of African ancestry
… and aligned to the hg19 reference genome using GATK and VariantMetaCaller. Bioinformatics analysis Variant annotation was performed using Annovar and the annotated variants were filtered based in rarity and pathogenicity. Tests for genetic differentiation and principle component analysis was …