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GWAS

Available Parameters

  • META_DATA_FILE Mandatory. The path to the metadata file (see below). Can be a path relative to the gwas folder next to the parameters file or an absolute file.
  • DATA_LOCATION Default: parent directory of the metadata file. The directory that functions as the path against which the data files referenced in the metadata file are to be found.
  • HG_VERSION Default: 19. Either 18 or 19. The reference assembly to use.

Metadata file

A TSV that functions as an index for several analyses in the same study. This pipeline uses the following mandatory columns:

  • STUDY Mandatory. The name of the study (max: 50 characters).
  • DATA_TYPE Mandatory. Must be GWAS.
  • ANALYSIS_NAME Mandatory. A short name for the analysis. It should not include the string "test" (or any variant where one or more of the characters are uppercase), otherwise the analysis will not show up in GWAVA. Max: 500 characters. The tuple (STUDY, ANALYSIS_NAME) must be unique.
  • INPUT_FILE. Mandatory. The name of the file containing the analysis' data.

Other columns can provide more meta data about the analysis. The full list can be seen by looking at the example file.

Analyses Data File

An example analysis data file can be found here. No column is mandatory, except for RS_ID. However, the P_VALUE should also be given for most functionality to work. Alleles may contain only one character.