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Varan
Michal J. Gajda edited this page Oct 28, 2020
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Varan is an application for analyzing variants. It reads input in mpileup format and can output a variety of global and per-site statistics. This is a work in progress, please contact me if you are interested in using it.
Varan can calculate ESI, the expected information to be gained from genotyping a site. This is useful for selecting divergent or diagnostic SNPs, and avoids some of the problems of using traditional measures, like p-values or F_ST.
Varan can also calculate traditional measures like nucleotide divserity or F_ST, and some novel ones, per site or globally. See the README or the --help output for more up-to-date information.
If you use varan, please cite the article.