QCTOOL specifications


Unique identifier OMICS_04411
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.4
Stability Stable
Maintained Yes


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QCTOOL in publications

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

[…] 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 0.05 and a minor-allele frequency corresponding to at least one chromosome in the whole material. the final data included […]

PMCID: 5482150
PMID: 28586055
DOI: 10.3892/mmr.2017.6663

[…] (affymetrix; thermo fisher scientific inc.) and then scanned using a scanner 3000 7g 4c (affymetrix; thermo fisher scientific inc.). quality control analysis was performed using the affymetrix mirna qctool (affymetrix; thermo fisher scientific inc.). for each mirna, multiple probes were spotted on the array, and the mean intensity of these probes was calculated to represent the expression value […]

PMCID: 5449482
PMID: 28620303
DOI: 10.3389/fphar.2017.00323

[…] 1000 genomes phase i data set (release date june 2014). imputed variants with an information score <0.8, maf <1%, hwe <0.0001 and genotyping success rate <95% were excluded using qctool, leaving a total of 1400 snps harboring the cyp4f12-cyp4f2-cyp4f11 genomic region., statistical analyses were conducted with the software package spss, version 18. for each univariate test […]

PMCID: 5411756
PMID: 28334860
DOI: 10.1093/hmg/ddx061

[…] quality control (qc) procedures were applied, as detailed in the ., genotype imputation was performed using impute2 (), with 1000 genomes project haplotypes (march 2012) as the reference panel. the qctool software was used to exclude snps with an ‘info’ score of <0.9. gtool software was then used to transform the imputed data to ped format, with a posterior probability of 0.9 used […]

PMCID: 5300907
PMID: 27863252
DOI: 10.1016/j.cell.2016.10.042

[…] a modified version of the impute2 software (), in chunks of 2mb with a 250kb buffer region. post-imputation, variants with maf < 0.00001 (1 in 100,000) were filtered from the dataset using qctool (http://www.well.ox.ac.uk/∼gav/qctool/), leaving 72,355,667 variants for analysis in the dataset., prior to imputation, additional variant qc steps were performed to establish a high quality […]

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