optiCall uses both within and across sample intensity information to accurately ascertain genotypes from across the minor allele frequency spectrum.

optiCall works by first taking a random subset of intensity measures, both within and across samples. The subset is used to define regions of high probability for the three genotype classes. Genotypes are then called on a per SNP basis, with all samples overlaid onto the probability regions, which are incorporated as a data-derived.prior during clustering. In this way common variants are seen as three clouds in a per SNP view, and rare variants are called based on the intensity region in which they fall.

Download and Installation

optiCall source code and documentation can be found on Bitbucket

License and Citation

optiCall is free and open source software, made available under the permissive MIT License.


For questions or suggestions/feedback, drop us an email at opticall@sanger.ac.uk.


Sanger Contributors


  • optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants.

    Shah TS, Liu JZ, Floyd JA, Morris JA, Wirth N et al.

    Bioinformatics (Oxford, England) 2012;28;12;1598-603