optiCall

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

It 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.

[Genome Research Limited]

Download

optiCall is freely available to use and modify on bitbucket

Calling a SNP with optiCall.

Calling a SNP with optiCall. [optiCall]

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License

Copyright © 2011 Tejas Shah & Carl Anderson Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Publications

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

    Shah TS, Liu JZ, Floyd JA, Morris JA, Wirth N, Barrett JC and Anderson CA

    Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.

    Motivation: Existing microarray genotype-calling algorithms adopt either SNP-by-SNP (SNP-wise) or sample-by-sample (sample-wise) approaches to calling. We have developed a novel genotype-calling algorithm for the Illumina platform, optiCall, that uses both SNP-wise and sample-wise calling to more accurately ascertain genotypes at rare, low-frequency and common variants.

    Results: Using data from 4537 individuals from the 1958 British Birth Cohort genotyped on the Immunochip, we estimate the proportion of SNPs lost to downstream analysis due to false quality control failures, and rare variants misclassified as monomorphic, is only 1.38% with optiCall, in comparison to 3.87, 7.85 and 4.09% for Illuminus, GenoSNP and GenCall, respectively. We show that optiCall accurately captures rare variants and can correctly account for SNPs where probe intensity clouds are shifted from their expected positions. Availability and implementation: optiCall is implemented in C++ for use on UNIX operating systems and is available for download at http://www.sanger.ac.uk/resources/software/opticall/.

    Funded by: Medical Research Council: G1001799; Wellcome Trust: 098051

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

Contact

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

* quick link - http://q.sanger.ac.uk/jhpo92yg