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ANNOVAR

ANNOVAR annotates genetic variants detected from a diverse set of genomes.

ANNOVAR is available as a module on Apocrita.

Usage

To run the default installed version of ANNOVAR, simply load the annovar module:

module load annovar

For usage documentation, pass the --help switch to any ANNOVAR binary for example, convert2annovar.pl --help.

Example jobs

Serial jobs

Here is an example job to perform a gene-based annotation, running on 1 core and 1GB of memory:

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G   # Request 1GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load annovar

annotate_variation.pl --geneanno \
                      --dbtype refGene \
                      --buildver hg19 \
                      --out example \
                      example.avinput \
                      humandb/

Here is an example job to convert a VCF file into an ANNOVAR input file format, running on 1 core and 1GB memory:

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G   # Request 1GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load annovar

convert2annovar.pl -format vcf4 \
                   -outfile example.out \
                   example.vcf

Reference