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, hs1 (T2T-CHM13) as well as mouse, worm, fly, yeast and many others).
Documentation
Databases
A few databases have been downloaded from the ANNOVAR site and put in the ${ANNOVAR_DATA} directory. Additional databases can be installed upon request.
Slurm script
The commands here are taken from the ANNOVAR tutorial using the input files found in ${ANNOVAR_HOME}/example.
#!/bin/bash
#SBATCH --job-name=annovar
#SBATCH --time=1:00:00
#SBATCH --partition=norm
#SBATCH --ntasks=8
#SBATCH --mem=32GB
module load annovar
table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation gx,r,f,f,f -nastring . -csvout -polish -xref example/gene_xref.txt
table_annovar.pl ex1.avinput ${ANNOVAR_DATA}/hg38 \
--thread $SLURM_NPROCS \
--buildver hg38 \
--outfile ex1.out \
--remove \
--protocol gene,clinvar_20220320,cosmic70,ljb26_all,avsnp150,cadd_1.5 \
--operation g,f,f,f,f,f \
--nastring '' \
-csvout -polish \
-xref example/gene_xref.txt
Build instructions for those who are curious
Register for the download at https://www.openbioinformatics.org/annovar/annovar_download_form.php
Receive a download link & download.
Extract to the /mnt/nasapps/production/annovar directory.
Software is a set of perl scripts. No compilation is required.
Download a sample set of databases:
$ cd ${ANNOVAR_DATA}
$ annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene hg19/
$ annotate_variation.pl -buildver hg19 -downdb cytoBand hg19/
$ annotate_variation.pl -buildver hg19 -downdb -webfrom annovar exac03 hg19/
$ annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avsnp147 hg19/
$ annotate_variation.pl -buildver hg19 -downdb -webfrom annovar dbnsfp30a hg19/