Software: ANNOVAR
Description
ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
Available Versions
Unspecified: | 2022-01-13 |
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For more information, please check its website: https://annovar.openbioinformatics.org/en/latest/.
Commands
- annotate_variation.pl
- coding_change.pl
- convert2annovar.pl
- retrieve_seq_from_fasta.pl
- table_annovar.pl
- variants_reduction.pl
Module
You can load the modules by:
module load biocontainers
module load annovar
Example job
Using
#!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bash
instead.
To run ANNOVAR on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=annovar
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers annovar
annotate_variation.pl --buildver hg19 --downdb seq humandb/hg19_seq
convert2annovar.pl -format region -seqdir humandb/hg19_seq/ chr1:2000001-2000003