atks / vt

A tool set for short variant discovery in genetic sequence data.
http://genome.sph.umich.edu/wiki/vt
MIT License
192 stars 3 forks source link
variant-calling

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