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http://hdl.handle.net/10609/127089
Title: | Comparación de diferentes métodos de calling de variantes somáticas: Mutect2, SomaticSniper, Varscan2 y Strelka2 |
Author: | Garrote Fernández, Sonia María |
Tutor: | Sastre Tomas, Jaume |
Others: | Maceira, Marc |
Abstract: | Genome sequencing has been extensively applied to the study of the cancer genomes. 'Calling' or 'Variant Calling' is a process used for the detection of the genetic variation, this could be applied to detection of genes responsible for the development and progression of cancer. There are some methods that implement this process. Each method has its own search algorithm, and it is usual that the results of one method differ from the other. In this study we focus on the discovery of somatic mutations in cancer genomes. The methods and results of some programs (Mutect2, SomaticSniper, Varscan2 y Strelka2) are analyzed. Hg38 reference genome is used. We made individual analysis of variant calling tools and the methods they apply. Doing Test and comparing those tools with tumor-normal samples. There were no coincidences between Mutect2 and VarScan2, there was 17 coincidences between Mutect2 and SomaticSniper, and 24 between Mutect2 and Strelka2; VarScan2 had only 1 coincidence with SomaticSniper in Mode 1; SomaticSniper had 38 coincidences with Strelka2 in Mode 1 and 31 in Mode 2. The results from the variant callers agree only on a subset of variants. |
Keywords: | cancer genetics variant calling |
Document type: | info:eu-repo/semantics/masterThesis |
Issue Date: | Jan-2021 |
Publication license: | http://creativecommons.org/licenses/by-nc-nd/3.0/es/ |
Appears in Collections: | Trabajos finales de carrera, trabajos de investigación, etc. |
Files in This Item:
File | Description | Size | Format | |
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sgarrotefTFM0121memoria.pdf | Memoria del TFM | 5,06 MB | Adobe PDF | View/Open |
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