vt

A tool set for short variant discovery in genetic sequence data.

Visit http://genome.sph.umich.edu/wiki/vt for instructions.

vt uses htslib¹, tclap², Rmath³, pcre2⁴ and libsvm⁵.

How to cite

vt normalize :
Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. Unified Representation of Genetic Variants. Bioinformatics (2015) 31(13): 2202-2204

Reference

1. https://github.com/samtools/htslib
2. http://tclap.sourceforge.net
3. https://github.com/atks/Rmath
4. http://sourceforge.net/projects/pcre
5. Chih-Chung Chang and Chih-Jen Lin, LIBSVM : a library for support vector machines. ACM Transactions on Intelligent Systems and Technology, 2:27:1--27:27, 2011. https://github.com/cjlin1/libsvm