optiCall is a robust genotype-calling algorithm for calling rare, low-frequency and common variants from SNP microarray intensity data.

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.


optiCall source code and documentation can be found on Bitbucket

Further information

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


If you need help or have any queries, please contact us using the details below.

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

Sanger Institute Contributors

Photo of Dr Carl Anderson

Dr Carl Anderson

Head of Human Genetics and Senior Group Leader

Previous contributors

Photo of Tejas Shah

Tejas Shah

Senior Computer Biologist