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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 [http://genome.sph.umich.edu/wiki/VcfCodingSnps] 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 [https://statgen.sph.umich.edu/wiki/Rare_variant_tests_implementation] to look for more features.
/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 [http://genome.sph.umich.edu/wiki/VcfCodingSnps] 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 [https://statgen.sph.umich.edu/wiki/Rare_variant_tests_implementation] to look for more features.
