Difference between revisions of "Example"

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(Created page with '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 [h…')
 
 
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You can return to the syntax wiki page [https://statgen.sph.umich.edu/wiki/Rare_variant_tests_implementation] to look for more features.
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You can return to the syntax wiki page [http://genome.sph.umich.edu/wiki/RvTests] to look for more features.

Latest revision as of 15:39, 30 January 2011

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.