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.
|Number of pages||5|
|State||Published - 2014|
Bibliographical noteFunding Information:
We graciously acknowledge the resources provided for this work by grants from the NIH (R01AG042611), the Alzheimer’s Association (MNIRG-11-205368), and startup funds from Brigham Young University.
© 2014 Ebbert et al.; licensee BioMed Central Ltd.
ASJC Scopus subject areas
- Structural Biology
- Molecular Biology
- Computer Science Applications
- Applied Mathematics