ANNOVAR Annotation of multiple VCF files error because of the absence of hg38_gnomad211_genome.txt file.

Question

[Can Abdullah]

I am trying to perform annotation for the first time but cannot due to some lack of files. I have just downloaded ANNOVAR and I think everything is up-to-date. (Actually, I want to work with the latest version of reference files) Here is my command and I get the following error:

mkdir -p /home/cancam/Desktop/THESIS\ PROJECT/VCF\ CAGI6\ Annotation\ Outputs/
for file in /home/cancam/Desktop/THESIS\ PROJECT/VCF\ CAGI6\ renamed/*.vcf; do
    /home/cancam/Desktop/THESIS\ PROJECT/annovar/table_annovar.pl "$file" /home/cancam/Desktop/THESIS\ PROJECT/annovar/humandb/ -buildver hg38 -out /home/cancam/Desktop/THESIS\ PROJECT/VCF\ CAGI6\ Annotation\ Outputs/"$(basename "$file" .vcf)" -remove -protocol refGene,gnomad211_genome -operation g,f -nastring .
done

NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)
Error: the required database file /home/cancam/Desktop/THESIS PROJECT/annovar/humandb/hg38_gnomad211_genome.txt does not exist.

In ANNOVAR website, it says:

Several very commonly used annotation databases for human genomes are additionally provided below. In general, users can use -downdb -webfrom annovar in ANNOVAR directly to download these databases.

But I could not do it. Can you please help me. Thank you!

Answer 1

[Ming Tommy Tang]

you can download it here https://gnomad.broadinstitute.org/downloads