ANNOVAR Annotation of multiple VCF files error because of the absence of hg38_gnomad211_genome.txt file.
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 annovarin ANNOVAR directly to download these databases.
But I could not do it. Can you please help me. Thank you!
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1 answer
you can download it here https://gnomad.broadinstitute.org/downloads
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