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