154    ◾    Bioinformatics

annotate_variation.pl -webfrom annovar -downdb avdblist -buildver

hg19 dblist

The list of the databases of the hg19 build will be saved in a file “hg19_avdblist.txt” in

“dblist” subdirectory. You can open that file and study the available annotation databases.

The “-webfrom” argument specifies the source of database; the values can be “ucsc”,

“annovar”, or a URL where the database is available.

The “-downdb” argument is the command to download an annotation database from

the source specified by “-webfrom”.

The “-buildver” argument specifies the genome build version (e.g., hg19).

For example, the following command downloads some annotation databases for hg19

build and they will be stored in “humandb” directory:

To download the gene-based annotation database for human variants:

annotate_variation.pl \

-buildver hg19 \

-downdb \

-webfrom annovar refGene humandb/

To download region-based annotation (cytogenetic bands) database of the human genome:

annotate_variation.pl \

-buildver hg19 \

-downdb cytoBand humandb/

To download filter-based ExAC (Exome Aggregation Consortium) annotation database:

annotate_variation.pl \

-buildver hg19 \

-downdb \

-webfrom annovar exac03 humandb/

To download the filter-based NCBI dbSNP annotation database (version 147):

annotate_variation.pl \

-buildver hg19 \

-downdb \

-webfrom annovar avsnp147 humandb/

To download the filter-based dbNSFP annotation database, which was developed for func-

tional prediction and annotation of all potential nonsynonymous SNVs in the human

genome:

annotate_variation.pl \

-buildver hg19 \