From Genome Analysis Wiki
Jump to navigationJump to search

An example is included in


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.