FreeBayes
Haplotype based variant finding with FreeBayes.
Requires Geneious 10.0+
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.
1.1 (15 Nov 2017) – Download for Geneious 10
– Upgraded FreeBayes to version 1.1
1.0 (05 Feb 2014) – Download
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012