FreeBayes

Haplotype based variant finding with FreeBayes.

Download plugin

Requires Geneious 10.0+

    FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.This plugin allows you to run FreeBayes on individual samples.

    Quick Start

    Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).

    Once installed, run the plugin by selecting a reference assembly and choosing Annotate & Predict - Find Variations/SNPs with FreeBayes... from the menu. Results are saved as annotations on your sequence.

    History

    1.1 (15 Nov 2017) – Download for Geneious 10

    – Upgraded FreeBayes to version 1.1

    1.0 (05 Feb 2014) – Download

    Citing

    Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012