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QCTOOL is a tool to administrate and quality control data from genome-wide associations studies (GWAS). The QCTOOL algorithm has functions for computing variant, sample QC metrics, for filtering, merging datasets, format conversion, annotation, LD between variants, genotype comparison, relatedness, principal components, genetic risk predictor scores, Hardy-Weinberg Equilibrium test, and multiple ways to manipulate the datasets.


GWAS study



Wigginton JE, Cutler DJ, Abecasis GR "A note on exact tests of Hardy-Weinberg equilibrium" Am J Hum Genet. 2005 May;76(5):887-93.
PMID: 15789306
PMCID: PMC1199378

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