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annovar_installation.md

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Annovar installation

  1. Unpack the package and add ANNOVAR into your system executable path

    tar xvfz annovar.latest.tar.gz
export PATH="/dir/annovar/:$PATH"

  2. First you need to create directories for saving Annovar databases files used for the annotation:

    • Create a folder (genomedb) for saving all Annovar databases, e.g. hg19db
    • Create a subfolder (seqFolder) for saving the reference genome, e.g. hg19db/hg19_seq

  3. Download the reference genome (by chromosomes) from UCSC for all desired builds as follows:

    annotate_variation.pl -buildver <build> -downdb seq <seqFolder>

    build is your prefered reference genome
    seqFolder is the location where the sequences (by chromosmes) should be stored, e.g. hg19db/hg19_seq

  4. Download all desired databases for your builds. At least the database refGene must be downloaded.

    annotate_variation.pl -buildver <build> -webfrom annovar -downdb <database> <genomedb>

    build is your prefered reference genome
    database is the name of database file to download, e.g. refGene
    genomedb is the location where all database files should be stored, e.g. hg19db

    The list of available Annovar databases can be found here: http://annovar.openbioinformatics.org/en/latest/user-guide/download/

  5. Edit the file build_listAVDB.txt present in mutspec folder to reflect the name and the type of the databases you have installed