TY - JOUR
T1 - Variant tool chest
T2 - An improved tool to analyze and manipulate variant call format (VCF) files
AU - Ebbert, Mark T.W.
AU - Wadsworth, Mark E.
AU - Boehme, K. L.
AU - Hoyt, Kaitlyn L.
AU - Sharp, Aaron R.
AU - O'Fallon, Brendan D.
AU - Kauwe, John S.K.
AU - Ridge, Perry G.
N1 - Publisher Copyright:
© 2014 Ebbert et al.; licensee BioMed Central Ltd.
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
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U2 - 10.1186/1471-2105-15-S7-S12
DO - 10.1186/1471-2105-15-S7-S12
M3 - Article
C2 - 25080132
AN - SCOPUS:84988360744
SN - 1471-2105
VL - 15
SP - 1
EP - 5
JO - BMC Bioinformatics
JF - BMC Bioinformatics
ER -