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VaRank: An integrated tool for SNV/indel annotation and ranking

https://lbgi.fr/VaRank/

QUICK INSTALLATION

  1. The sources can be cloned to any directory:
cd /path/to/install/
git clone [email protected]:lgmgeo/VaRank.git
  1. Set the VARANK global environmental variable as the location of the git repo on your system.

In csh:

setenv VARANK /path/to/install/VaRank/

In bash:

export VARANK=/path/to/install/VaRank
  1. Set the ALAMUT/SNPEFF global environmental variable. Depending on the selected annotation engine:
  • $ALAMUT: Alamut Batch installation directory
  • $SNPEFF: SnpEff and SnpSift installation directory

TEST with the Alamut annotation engine

  1. Change to the repo directory, look at the configfile and run the test
cd $VARANK/Tests/Alamut/

cat configfile

$VARANK/bin/VaRank -vcfDir "." -SamOut "Sample1 Sample2"
  1. Examine the outputs (*tsv)