Comparison of sequencing data processing pipelines and application to underrepresented African human populations.

ABSTRACT:

Background

Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its "Best Practices" bioinformatic pipelines. However, studies often focus on a few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratifica

SUBMITTER: Breton G 

PROVIDER: S-EPMC8502359 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature