GTOOL protocols

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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

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Maintainer


  • person_outline Colin Freeman <>

GTOOL in pipelines

 (8)
2017
PMCID: 5669488
PMID: 29066854
DOI: 10.1038/jhg.2017.76

[…] after imputation, snps were filtered based on the mendelian error rate in families, which was calculated from the best guess genotypes in families (trios or sib-pairs with parents) using first gtool to calculate best guess genotypes and then plink 1.07 to analyze the data. snps were removed if the mendelian error rate >0.02, the imputed allele frequency differed more than 0.15 […]

2017
PMCID: 5727191
PMID: 29234017
DOI: 10.1038/s41467-017-02182-z

[…] data (hg19/1000 genomes mar 2012 eur)., 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, […]

2016
PMCID: 5007453
PMID: 26989097
DOI: 10.1192/bjp.bp.115.168229

[…] with concurrent phasing. snps imputed with an info metric >0.8 and a minor allele frequency (maf) >1% were considered best-guess genotypes, and converted back to plink binary format using gtool (freeman and marchini, available at www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html). snps with a genotype probability of <0.9 were set as missing, and those present in <98% […]

2015
PMCID: 4564946
PMID: 26014426
DOI: 10.1038/ejhg.2015.102

[…] humanhap1.2m duo 1m arrays. imputation was done in two datasets (n=2040 from the humanhap300 array; n=3614 from the humanhap610q, humanhap1m duo and 1.2m duo 1m arrays) which were then merged with gtool. we performed imputation for twins uk study subjects based on 1000 genomes data as described previously. this involved estimating the phase of contiguous variants in the subjects using […]

2015
PMCID: 4584317
PMID: 26184321
DOI: 10.3390/genes6030559

[…] snps were filtered based on the mendelian error rate in families. the mendelian error rate was calculated on the best guess genotypes in families (trios and sib-pairs with parents) using first gtool to calculate best guess genotypes and then plink 1.07 to analyze the data. snps were removed if the mendelian error rate >2%, if the imputed allele frequency differed more than 0.15 […]


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GTOOL in publications

 (33)
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] 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 […]

PMCID: 5882890
PMID: 29615742
DOI: 10.1038/s41598-018-23860-y

[…] 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 […]

PMCID: 5876265
PMID: 29404672
DOI: 10.1007/s00125-018-4555-9

[…] allele > effect alleleassociations were tested using qlim procedure in sas v9.4 (sas, cary, nc, usa), and are based on extracted genotypes from dosage data according to the best guess using gtool v0.7.5 (www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html) adjusting for sex, age at diagnosis, type 1 diabetes duration and cohort (primary vs secondary)β, β coefficient; f, fasting; s, […]

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

[…] 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. […]

PMCID: 5747239
PMID: 29284405
DOI: 10.1186/s12864-017-4390-2

[…] (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 […]


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