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Protocols

Gencall specifications

Information


Unique identifier OMICS_02584
Name Gencall
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Biological technology Illumina
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability No
Maintained No

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Gencall citations

 (104)
library_books

Human Genetic Susceptibility to Native Valve Staphylococcus aureus Endocarditis in Patients With S. aureus Bacteremia: Genome Wide Association Study

2018
Front Microbiol
PMCID: 5893849
PMID: 29670602
DOI: 10.3389/fmicb.2018.00640

[…] The Netherlands (Prof. Dr. André Uitterlinden), according to the manufacturer’s protocols.A genotyping report was produced in GenomeStudio V2011.1. Low quality SNPs were removed based on the Illumina GenCall (<0.1), call rate lower than 97%, Hardy–Weinberg equilibrium deviations with p < 7 × 10-8, minor allele frequencies (MAF) smaller than 0.01 or being monomorphic loci. Low quality samples were […]

library_books

A transcriptome wide association study identifies PALMD as a susceptibility gene for calcific aortic valve stenosis

2018
Nat Commun
PMCID: 5840407
PMID: 29511167
DOI: 10.1038/s41467-018-03260-6

[…] erformed using the Illumina HumanOmniExpress BeadChip. Standard genotyping QCs were performed. SNP genotyping data were filtered for call rate < 97%, low-quality loci with 10th percentile of Illumina GenCall score ≤ 0.1, Hardy-Weinberg equilibrium P < 1 × 10−7, MAF < 1%, and different call rate between cases and controls (P < 1 × 10−6). A total of 613,862 SNPs passed QC checks. Samples were exclud […]

library_books

Ovarian cancer risk, ALDH2 polymorphism and alcohol drinking: Asian data from the Ovarian Cancer Association Consortium

2018
Cancer Sci
PMCID: 5797830
PMID: 29247577
DOI: 10.1111/cas.13470

[…] s conducted using a custom Illumina Infinium array (iCOGS; Illumina, San Diego, CA, USA) across two centers, of which 44 308 passed quality control. Genotypes were called using Illumina's proprietary GenCall algorithm. Standard quality control measures were applied across all SNP and all samples. Samples were excluded for any of the following reasons: genotypically not female XX (XY, XXY or XO); o […]

library_books

Meta analysis of genome wide association studies identifies 8 novel loci involved in shape variation of human head hair

2017
Hum Mol Genet
PMCID: 5886212
PMID: 29220522
DOI: 10.1093/hmg/ddx416

[…] na 317, 370, 610, 660, Core + Exome, PsychChip, Omni2.5 and OmniExpress SNP chips which included data from twins, their siblings and their parents. Genotype data were screened for genotyping quality (GenCall < 0.7), SNP and individual call rates (< 0.95), HWE failure (P < 1e-6) and MAF (< 0.01). As these samples were genotyped in the context of a larger project, the data were integrated with the l […]

call_split

Evaluating the glucose raising effect of established loci via a genetic risk score

2017
PLoS One
PMCID: 5681259
PMID: 29125842
DOI: 10.1371/journal.pone.0186669
call_split See protocol

[…] ped 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 discrepancies, ethnic outlie […]

call_split

Hair Cortisol in Twins: Heritability and Genetic Overlap with Psychological Variables and Stress System Genes

2017
Sci Rep
PMCID: 5703444
PMID: 29127340
DOI: 10.1038/s41598-017-11852-3
call_split See protocol

[…] performed using the Illumina Human610-Quad and Core+Exome SNP chips. Quality control included inspection of pedigree, sex, Mendelian errors, and ancestry, as well as filtering for genotyping quality (GenCall <0.7); SNP and individual call rates (<0.95); Hardy-Weinberg equilibrium failure (P <10–6); and minor allele frequency (<0.01). Subjects were imputed to the Haplotype Reference Consortium (HRC […]

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