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 git@github.com:lgmgeo/VaRank.git

2. 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

3. 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" 

2. Examine the outputs (*tsv)