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jlim [2016/11/18 16:16]
schun created
jlim [2016/11/18 16:19]
schun [How to run JLIM on your data]
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 </​code>​ </​code>​
   * Generate secondary trait genotypes (.ped.gz files).   * Generate secondary trait genotypes (.ped.gz files).
-  * Generate secondary trait association and mperm files. For example, ​``` plink --bfile region1 --pheno gene1tx.pheno --linear --out LCL.gene1 --covar yourcov\\ +  * Generate secondary trait association and mperm files. For example, ​ 
---mperm 1000 --merpm-save-all --chr yourCHR --from-bp yourSTARTBP --end-bp yourENDBP+<​code>​ 
 +plink --bfile region1 --pheno gene1tx.pheno --linear --out LCL.gene1 --covar yourcov --mperm 1000 --merpm-save-all --chr yourCHR --from-bp yourSTARTBP --end-bp yourENDBP
  
 gzip LCL.gene1.assoc.linear gzip LCL.gene1.assoc.linear
  
-gzip LCL.gene1.mperm.dump.all ​``` - Run jlim_gencfg.sh and run_jlim.sh similarly as the above.+gzip LCL.gene1.mperm.dump.all 
 +</​code>​ 
 +  * Run jlim_gencfg.sh and run_jlim.sh similarly as the above.