Annovar installation:
====================



1) Download latest annovar by registering here : http://www.openbioinformatics.org/annovar/annovar_download_form.php 

	Downloaded archive file should contain all perl scripts necessary to run annovar ( eg: annovar.latest.tar.gz )

2) Decompress the archive using following command:

	tar -xvf annovar.latest.tar.gz

	This will generate a directory named "annovar" which contain perl scripts and databases.
        
        You should see following files/directories in "annovar" directory:
        annotate_variation.pl
        coding_change.pl
        convert2annovar.pl
        example
        humandb
        retrieve_seq_from_fasta.pl
        table_annovar.pl
        variants_reduction.pl
    

3)Installing necessary databases:

cd annovar  ( ie, go to the directory where annovar scripts are installed)

run the following scripts and wait for downloads to complete

./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/
./annotate_variation.pl -buildver hg19 -downdb cytoBand humandb/
./annotate_variation.pl -buildver hg19 -downdb genomicSuperDups humandb/ 
./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar esp6500siv2_all humandb/
./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar 1000g2015aug humandb/
./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar exac03 humandb/ 
./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avsnp147 humandb/ 
./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar dbnsfp30a humandb/


Above commands will download and setup all necessary databases and indexes in  humandb/ directory. This includes following files:

annovar_downdb.log              hg19_esp6500siv2_all.txt
hg19_AFR.sites.2015_08.txt      hg19_esp6500siv2_all.txt.idx
hg19_AFR.sites.2015_08.txt.idx  hg19_EUR.sites.2015_08.txt
hg19_ALL.sites.2015_08.txt      hg19_EUR.sites.2015_08.txt.idx
hg19_ALL.sites.2015_08.txt.idx  hg19_exac03.txt
hg19_AMR.sites.2015_08.txt      hg19_exac03.txt.idx
hg19_AMR.sites.2015_08.txt.idx  hg19_genomicSuperDups.txt
hg19_avsnp147.txt               hg19_refGeneMrna.fa
hg19_avsnp147.txt.idx           hg19_refGene.txt
hg19_cytoBand.txt               hg19_refGeneVersion.txt
hg19_dbnsfp30a.txt              hg19_SAS.sites.2015_08.txt
hg19_dbnsfp30a.txt.idx          hg19_SAS.sites.2015_08.txt.idx
hg19_EAS.sites.2015_08.txt      hg19_seq
hg19_EAS.sites.2015_08.txt.idx


 
Quick start guide:
http://www.openbioinformatics.org/annovar/annovar_startup.html