Journal Article

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files

Hoyt, Kaitlyn L, Wadsworth, Mark E, Ridge, Perry G, Kauwe, John SK, Boehme, Kevin L, O'Fallon, Brendan D, Ebbert, Mark TW, Sharp, Aaron R

2014

Overview

Background Since the advent of next-generation sequencing many previously untestable hypotheses have been realized. Next-generation sequencing has been used for a wide range of studies in diverse fields such as population and medical genetics, phylogenetics, microbiology, and others. However, this novel technology has created unanticipated challenges such as the large numbers of genetic variants. Each caucasian genome has more than four million single nucleotide variants, insertions and deletions, copy number variants, and structural variants. Several formats have been suggested for storing these variants; however, the variant call format (VCF) has become the community standard. Results We developed new software called the Variant Tool Chest (VTC) to provide much needed tools to work with VCF files. VTC provides a variety of tools for manipulating, comparing, and analyzing VCF files beyond the functionality of existing tools. In addition, VTC was written to be easily extended with new tools. Conclusions Variant Tool Chest brings new and important functionality that complements and integrates well with existing software. VTC is available at https://github.com/mebbert/VariantToolChest

• Publisher: BioMed Central,Springer Nature B.V
• Subject: Algorithms / Bioinformatics / Biomedical and Life Sciences / Biotechnology / Chromosomes / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Databases, Genetic / Genetic variance / Genetic Variation / Genetics / Genome, Human / Genomes / Genotype / Genotype & phenotype / High-Throughput Nucleotide Sequencing - methods / Humans / Java / Life Sciences / Methods / Microarrays / Microbiology / Software / Studies / Writing