GTOOL pipeline

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

 (4)
2016
PMCID: 5007453
PMID: 26989097
DOI: 10.1192/bjp.bp.115.168229

[…] with concurrent phasing.28 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.13 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 […]

2011
PMCID: 3287839
PMID: 22373249
DOI: 10.1186/1753-6561-5-S9-S115

[…] 1.05 [8,9], to generate additive snp coding. for our analyses we implement cast [2], the cmc method [3], and the ws method [4] in r, version 2.12.0 [10]. the input data are further converted with gtool, version 0.5.0 [11], into the snptest format for running granvil, version 0.4, which is an implementation of rvt1 [12], and for running ccravat [13], an implementation of rvt2 [5]. granvil […]

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