Example

An example is included in

 /home/youna/prj/RV/RV3Tests.v1/example

where LDL.test.vcf is the annotated vcf file and LDL.test.log is the log from the annotation. We've used [1] for the annotation .

1. Prepare the input files using prepare012s

  prepare012s --vcf test.vcf --log test.log --All 0 --outputPrefix test --outputGeneList test.Gene

You can check if test.012, test.012.indv, test.012.pos, test.012.frq have been generated. 

2. Run rvTests using this line of code

 rvTests --genofile test.012 --geneList test.Gene --cutoff 0.05 --collapseChoice or 
  --phenofile y.txt --nPermute 1000 --geneGlobalTestOut globaltestOut.txt 
  --geneTestpvalueFile geneTestOut.txt

You can check if geneTestOut.txt or globaltestOut.txt are there.

You can return to the syntax wiki page [2] to look for more features.