GenoSNP statistics

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GenoSNP specifications

Information


Unique identifier OMICS_00722
Name GenoSNP
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Biological technology Illumina
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability No
Maintained No

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Publication for GenoSNP

GenoSNP in publications

 (16)
PMCID: 5681259
PMID: 29125842
DOI: 10.1371/journal.pone.0186669

[…] were genotyped using the illumina metabochip for the thiseas study and using the illumina humancoreexomechip at the wellcome trust sanger institute, hinxton, uk. the genotype calling algorithms were genosnp and gencall for thiseas and gomap studies respectively. for both studies we excluded individuals with sample call rate < 95%, genome-wide heterozygosity higher than ± 3sd, sex […]

PMCID: 4952362
PMID: 27435189
DOI: 10.1186/s13073-016-0329-5

[…] in two batches. these data have been deposited in the european genome-phenome archive (ega; accession number egas00001001251 []) and are available on request. genotype calls were made using genosnp software. processing of genotype data is described in additional file : supplemental methods., details of samples used in eqtl analyses are tabulated in additional file . cis-eqtl mapping […]

PMCID: 4921002
PMID: 27343118
DOI: 10.1186/s12863-016-0398-x

[…] needed to accurately infer genotypes. recently, several popular calling algorithms have been designed for illumina platform, such as: beagle with beaglecall software [], crlmm [, ], gencall [], genosnp [], and iluminus []. in general, illumina chip catalogs millions of snps and processes a large number of parallel samples, and the genotyping algorithms for the illumina data is of the main […]

PMCID: 4915815
PMID: 27324836
DOI: 10.7554/eLife.15266.040

[…] and is outlined in detail elsewhere (). briefly, genotype calls were formed by taking a consensus across three different calling algorithms (illuminus, gencall in illumina’s beadstudio software, and genosnp) () and were aligned to the forward strand. using the data from each country separately, snps with a minor allele frequency of <1% and missingness <5% were excluded, and additional qc […]

PMCID: 4629224
PMID: 26416757
DOI: 10.1038/nature15390

[…] and illumina humanomni2.5–8 (gambia, malawi) platforms. as described previously we used three different calling algorithms (illuminus, illumina’s gencall algorithm as provided in beadstudio, and genosnp), each of which uses slightly different information in the data. we formed final genotype calls by taking consensus between the three algorithms. genotypes where any two of the three calling […]


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GenoSNP institution(s)
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
GenoSNP funding source(s)
Supported by UK Engineering and Physical Sciences Research Council Life Sciences Interface Doctoral Training Studentships.

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