Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach

被引：0

作者：

Pinheiro, Miguel ^{[1
]}

Silva, Jorge Miguel ^{[2
]}

Oliveira, Jose Luis ^{[2
]}

机构：

[1] Univ Aveiro, Dept Med Sci, IBiMED, Aveiro, Portugal

[2] Univ Aveiro, IEETA, DETI, LASI, Aveiro, Portugal

来源：

BIOINFORMATICS AND BIOMEDICAL ENGINEERING, IWBBIO 2023, PT II | 2023年 / 13920卷

关键词：

Variant Calling; Genomics; Cohorts; Pipeline; FRAMEWORK; FORMAT;

D O I：

10.1007/978-3-031-34960-7_6

中图分类号：

R318 [生物医学工程];

学科分类号：

0831 ;

摘要：

The identification of genetic variations in large cohorts is a critical issue to identify patient cohorts, disease risks, and to develop more effective treatments. To help this analysis, we improved a variant calling pipeline for the human genome using state-of-the-art tools, including GATK (Hard Filter/VQSR) and DeepVariant. The pipeline was tested in a computing cluster where it was possible to compare Illumina Platinum genomes using different approaches. Moreover, by using a secure data space we provide a solution to privacy and security concerns in genomics research. Overall, this variant calling pipeline has the potential to advance the field of genomics research significantly, improve healthcare outcomes, and simplify the analysis process. Therefore, it is critical to rigorously evaluate these pipelines' performance before implementing them in clinical settings.

引用

页码：72 / 85

页数：14

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