A short unix shell script for vcftools commands iteration to obtain the genotypes of variations for forensic purpose. (December 2017)

• Record Type: Journal Article
• Authors: Zhao, Yuancun; Zhao, Xiaohong; Zhang, Shu; Gao, Zehua; Yang, Yiwen; Fang, Ting; Wang, Yufang; Zhang, Ji
• Is Part Of: Forensic science international. Volume 6(2017)
• Page Start: e49
• Page End: e51
• Publication Date: 2017-12
• Subjects: Shell script -- Genotype -- Population genetics; Forensic genetics -- Periodicals; Forensic Genetics -- Periodicals; Electronic journals; 614.1
• DOI: 10.1016/j.fsigss.2017.09.007
• Languages: English
• ISSNs: 1875-1768

Abstract

Abstract: The release of 1000 Genomes Project has provided a great variety of genome-wide variations spanning major populations worldwide, which offered a convenient path to the study of human genetic structure. VCFtools, a suite of functions dedicated to loci details summarizing, calculating, filtering, and genotype outputting can act as a powerful utility for genetic markers hunting and evaluating in the context of forensic purpose. While it is a labor-intensive and error-prone job involving repeating of multiple VCFtools commands step by step. Hence, we introduced a short UNIX-based bash shell script which contains an iteration structure to call VCFtools commands repeatedly for summarizing genotypes in different variation loci of different populations automatically. By setting up variations list and groups list, VCFtools commands with different arguments can be executed consecutively. Consequently, this process can be realized automatically with high efficiency and precision in the study of forensic genetics.