The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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SKAT

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Takes input files from the user, runs SKAT analysis on them, and outputs the results.

Quick Start

  • To use SKAT, import your data in binary (.bed, .bim, and .fam) format. You will also need a .SetID file, which simply groups SNPs based on location. Without this file, SKAT will not run. A covariates file and a phenotypes file can also be provided, but these are optional.

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> SKAT.

Input File(s)

Use Example1.bed, Example1.bim, Example1.fam, Example1.SetID, and Example1.Cov from the directory above as test input. These are small sample input files provided by the makers of SKAT, so the analysis should complete fairly quickly.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input files to get the output provided in the next section below.

Required Input Files
  • Select .bed file:
    • Example1.bed from the directory listed above.
  • Select .bim file:
    • Example1.bim from the directory listed above.
  • Select .fam file:
    • Example1.fam from the directory listed above.
  • Select .SetID file:
    • Example1.SetID from the directory listed above.
Covariates
  • Select the covariates file:
    • Example1.Cov from the directory listed above.
  • Column where names are found:
    • 1
  • Does your covariates file have a header?:
    • Yes
  • How is your covariates file formatted?:
    • space-delimited
Phenotypes
  • Leave everything blank (or default) for this section. This section is only required if your phenotypes are encoded separately from your other input files.
Experiment Design
  • Which type of test do you want to perform?:
    • Default
  • Kernel type:
    • Linear Weighted

Output Files

For the test case, the output file you will find in the example_data directory is named SKAT.unnamed.default.txt. For other analyses, expect a text file named SKAT.phenotype.kernel.txt as output, where "phenotype" is the name of the phenotype ("unnamed" if no phenotypes file was provided), and "kernel" is the type of kernel you selected ("default" or "weighted.burden").

SKAT will also output 4 other files, but these files are irrelevant to the results and can be ignored. These files are:

  • .SSD
  • .SSD.info
  • .SSD.info.TEMP.txt
  • .SSD_LOG.txt

Tool Source for App

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