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Allows genotype calling for the Illumina Infinium single nucleotide polymorphism (SNP) genotyping array. GenoSNP can call genotypes within-sample. The within-sample genotyping capability is advantageous for SNPs with very small minor allele frequencies where the existence of heterozygotes and minor allele homozygotes occur rarely. The software call probabilities are shown to be well calibrated enabling their use in downstream analyses such as phasing and genotype imputation. It could also make use of the information provided by samples ran simultaneously on the same array.

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GenoSNP classification

GenoSNP specifications

Software type:
Restrictions to use:
Academic or non-commercial use
Operating system:
Computer skills:
Command line interface
Biological technology:
Programming languages:

GenoSNP distribution


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GenoSNP support


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Department of Statistics, University of Oxford, Oxford, UK; Life Sciences Interface Doctoral Training Centre, University of Oxford, Wolfson Building, Parks Road, Oxford, UK; Genomics Group, Wellcome Trust Centre for Human Genetics, Oxford and MRC Mammalian Genetics Unit, MRC Harwell, Harwell, UK

Funding source(s)

Supported by UK Engineering and Physical Sciences Research Council Life Sciences Interface Doctoral
Training Studentships.

Link to literature

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