annovar
Link to section 'Introduction' of 'annovar' Introduction
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).
For more information, please check its website: https://annovar.openbioinformatics.org/en/latest/.
Link to section 'Versions' of 'annovar' Versions
- 2022-01-13
Link to section 'Commands' of 'annovar' Commands
- annotate_variation.pl
- coding_change.pl
- convert2annovar.pl
- retrieve_seq_from_fasta.pl
- table_annovar.pl
- variants_reduction.pl
Link to section 'Module' of 'annovar' Module
You can load the modules by:
module load biocontainers
module load annovar
Link to section 'Example job' of '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