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Citations per year

Number of citations per year for the bioinformatics software tool GTOOL
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This map represents all the scientific publications referring to GTOOL per scientific context
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Protocols

GTOOL specifications

Information


Unique identifier OMICS_04412
Name GTOOL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Colin Freeman

GTOOL citations

 (40)
library_books

Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

2018
Nat Commun
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] mes phase 1 imputed data from Blue Mountain Eye Study (BMES) population cohort comprising 2582 individuals of European ancestry to calculate linkage disequilibrium (LD) patterns. We used the software GTOOL-v0.7.5 (http://www.well.ox.ac.uk/%7Ecfreeman/software/gwas/gtool.html) to convert BMES IMPUTE2 data (both SNPs and Indels) to the plink format. This conversion changes A/T/G/C/I/D/R based allele […]

call_split

Systemic and specific effects of antihypertensive and lipid lowering medication on plasma protein biomarkers for cardiovascular diseases

2018
Sci Rep
PMCID: 5882890
PMID: 29615742
DOI: 10.1038/s41598-018-23860-y
call_split See protocol

[…] unks of around 5 M base pairs ensuring ≥200 genotyped SNPs in each chunk. The resulting data were filtered on marker level by requiring IMPUTE’s ‘info’ score > 0.3 in both cohorts before merging with GTOOL(v0.7.5) requiring a dosage threshold above 0.9 in at least 95% of the individuals. The merged data were filtered using QCTOOL (v1.4) requiring a Bonferroni corrected Hardy-Weinberg cut-off of 0. […]

library_books

Re analysis of public genetic data reveals a rare X chromosomal variant associated with type 2 diabetes

2018
Nat Commun
PMCID: 5778074
PMID: 29358691
DOI: 10.1038/s41467-017-02380-9

[…] ype imputation approach based on prephasing the study genotypes into full haplotypes with SHAPEIT2 to ameliorate the computational burden required for genotype imputation through IMPUTE2. We used the GTOOL software (http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html, version 0.7.5) to homogenize strand annotation by merging the imputed results obtained from each set of genotyped data. To […]

call_split

Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle

2017
BMC Genomics
PMCID: 5747239
PMID: 29284405
DOI: 10.1186/s12864-017-4390-2
call_split See protocol

[…] enotype (i.e. 0, 1 and 2), whereas IMPUTE2 outputs genotype likelihood only and FImpute outputs discrete genotypes only. To transform allele dosage data from IMPUTE2 to discrete genotypes the program GTOOL (version 0.7.5) was used [] applying the –G option. We did not want to have missing genotypes in our data. To achieve this the genotype likelihood threshold for calling a genotype was set to 0.3 […]

call_split

Protein quantitative trait locus study in obesity during weight loss identifies a leptin regulator

2017
Nat Commun
PMCID: 5727191
PMID: 29234017
DOI: 10.1038/s41467-017-02182-z
call_split See protocol

[…] Biology Workbench http://workbench.sdsc.edu;GCTA, http://cnsgenomics.com/software/gcta/; https://imputationserver.sph.umich.edu/index.html#!pages/home;GTOOL, http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html;GTEx database, http://www.gtexportal.org/home/;IPA, http://www.ingenuity.com/;Michigan Imputation Server, https://imputationserver.sp […]

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

[…] 3-way reference panel (1000Genomes (http://www.1000genomes.org/), UK10K (http://www.uk10k.org/) and MANOLIS study). Estimated probabilities for these SNPs were converted to best-guess genotypes using gtool (http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html). In the imputed format each SNP is represented as a set of three probabilities which corresponds to allele pairs AA, AB and BB. Usin […]


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