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Protocols

optiCall specifications

Information


Unique identifier OMICS_02585
Name optiCall
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Tejas. S. Shah

Publication for optiCall

optiCall citations

 (8)
library_books

Identification of new susceptibility loci for type 2 diabetes and shared etiological pathways with coronary heart disease

2017
Nat Genet
PMCID: 5844224
PMID: 28869590
DOI: 10.1038/ng.3943

[…] University of Cambridge, UK. In each study, samples with extreme intensity values, and outlying plates or arrays were removed prior to genotype calling. Genotype calling was initially performed with optiCall. Samples with call rate (CR) less than (mean CR - 3 standard deviations) were removed prior to post-processing optiCall calls with zCall. Scanner specific Z-values (calculated using 1,000 sam […]

library_books

Transancestral mapping and genetic load in systemic lupus erythematosus

2017
Nat Commun
PMCID: 5520018
PMID: 28714469
DOI: 10.1038/ncomms16021

[…] North Shore-LIJ Health System’s Feinstein Institute for Medical Research. Intensity data were generated for all samples and sent to the Oklahoma Medical Research Foundation for genotype calling using OptiCall. OptiCall default options were used with one exception: the ‘-nointcutoff’ option was included to allow removal of intensity outliers. Subsequent genotype clusters were viewed against their i […]

call_split

Association of IFIH1 and pro inflammatory mediators: Potential new clues in SLE associated pathogenesis

2017
PLoS One
PMCID: 5325200
PMID: 28234905
DOI: 10.1371/journal.pone.0171193
call_split See protocol

[…] Samples were genotyped on the Illumina ImmunoChip array on an Illumina iScan according to the manufacturers protocols []. Genotypes were called using Opticall [] using the default options with the addition of -nointcutoff option in order to manually remove intensity outliers. Genotype clusters were determined using Evoker []. Standard quality contr […]

library_books

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits

2016
Cell Rep
PMCID: 5130901
PMID: 27818087
DOI: 10.1016/j.celrep.2016.10.053

[…] Volunteers from the 500FG cohort were genotyped using the Illumina Human OmniExpress Exome-8 v1.0 SNP chip. The genotype was called with Opticall 0.7.0 using the default settings, excluding samples with a call rate ≤ 0.99. Variants with Hardy-Weinberg equilibrium (HWE) ≤ 0.0001, call rate ≤ 0.99, and minor-allele frequency (MAF) ≤ 0.00 […]

library_books

Genetic Evaluation of Schizophrenia Using the Illumina HumanExome Chip

2016
PLoS One
PMCID: 4814136
PMID: 27028512
DOI: 10.1371/journal.pone.0150464

[…] s (12 equals the number of samples per chip) were manually checked to exclude chip effects. All SNPs on the X and Y chromosome were manually verified. Genotypes were automatically clustered using the OPTICALL software, and Single Nucleotide Variants (SNV, both SNP and indels or deletions) with major differences in call rates between both methods were manually verified and excluded when after manua […]

library_books

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease specific patterns at shared loci

2016
Nat Genet
PMCID: 4848113
PMID: 26974007
DOI: 10.1038/ng.3528

[…] of a set of 14,484 independent (minor allele frequency (MAF)>0.05) SNPs excluding X- and Y-chromosomes, SNPs in LD (leaving no pairs with r2>0.2), and 11 high-LD regions as described by Price et al.. OptiCall genotype recalling was performed with a Hardy-Weinberg equilibrium P-value threshold of 10−15 for each batch, Hardy-Weinberg equilibrium blanking disabled and a genotype call threshold of 0.7 […]

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optiCall institution(s)
Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
optiCall funding source(s)
This work is funded by a grant from the Wellcome Trust (098051).

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