Allelic Test

#This is a demo file
#Usage: java -Xms1500m -Xmx2500m -jar GWASpi.jar script scriptFile [log cli.log]

Line by line…

Let’s look into the example above and explain it line by line:

  • First we see two lines starting with a "#" character. These are comment lines and you can have as many as you want, as long as they start with "#".
  • Next, the "data-dir=/GWASpi/data/" line specifies where GWASpi’s datae has to be stored. If the database doesn’t allready exist, a new and empty one will be created at the specified path.
  • Following these lines starts the "[script][/script]" block itself.
  • Next comes the call to the operation command, in this case 0.command=allelic_association

Following the operation call you will need to list a number of parameters. Each specific operation call has a given number and types of calls, which you will have to respect in name and order for the operation to run sucessfully:

  1. study-id= <- This is the Study ID of the study the new genotypes have to be loaded under.
  2. matrix-id= <- Indicate the genotype matrix the operation has to be performed uppon
  3. gtfreq-id= <- Indicate the id of the Genotype frequency operation the Allelic Association test has to be based on.
  4. hw-id= <- Indicate the id of the Hardy-Weinberg operation the Allelic Association test has to use for filtering.
  5. calculate-discard-threshold-for-HW= <- Boolean to toggle filter [true/false]
  6. discard-marker-with-provided-threshold= <- Boolean to toggle filter [true/false]
  7. discard-marker-HW-treshold= <- Specify value in case of discard-marker-with-provided-threshold