QUICKTEST 1.1

QUICKTEST is dedicated to association analysis between quantitative traits and uncertain
genotypes, for which it offers a rich suite of analysis methods. However, it has rather
limited facilities for analysis of binary or case/control phenotypes. The main features
are that quicktest:

  • Reads genotypes in the common file format as used by impute, snptest, and related software. For convenience, quicktest can successively read multiple genotype files (e.g. for separate chromosomes) and write all results to a single outputfile, and can also restrict analyses to SNPs from a prespecified list.
  • Reads phenotypes in either of two different formats:
    • the file format used by snptest
    • the file format generated by the R function write.table()
  • Offers a range of statistical methods for dealing with genotype uncertainty:
    • best guess genotypes (a.k.a. the calling method)
    • expected genotype dosages (a.k.a. the mean method)
    • a score test (the “-proper” method of snptest)
    • exact maximum likelihood
    • a Markov chain Monte Carlo method
  • Offers two optional methods for dealing with phenotypes that do not have an exactly normal distribution:
    • Quantile–quantile transformation, which uses only the ranks of observations
    • A Gaussian mixture model based method that uses the full data
  • Can run permutation tests, either using an adaptively chosen number of permutations, or using the same ensemble of phenotype permutations for all SNPs
  • Can test for interaction between each SNP and a covariate. This can be used to test for GxE, or for GxG between all SNPs and a single SNP
  • Runs much faster than snptest, for an equivalent analysis
  • Is freely available, including source code, under the terms of the GNU GPL

The current limitations are that quicktest:

  • Has poor facilities for analysis of binary phenotypes
  • Does not allow non-additive genetic models
  • With the exceptions of interaction and binary trait analyses, other quantitative

trait analyses do not take covariates into account on a SNP by SNP basis. In-
stead, a univariate “residual phenotype” is constructed once, and then used for all
association tests.

Accessing the software

To load the module:

$ module load apps/quicktest/1.1

An example command to include in your job script:

quicktest --pheno <phenotype_file> --out <output_file>

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the QUICKTEST website for more information regarding this application.


Last modified: 15 December 2017