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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 latest 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 memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

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
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load annovar

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

Reference