How to use GRCh38 as reference for Annotating the variants using Annovar?

Question

[Karma]

I want to annotate my vcf file using Annovar and GRCh38 as reference. Does annovar supports GRCh38? How can I use GRCh38 for annotating my vcf file?

[naiem2217]

#Download dataset of hg38 required for annotate vcf file ; prior to this make a "humandb" folder where data will be downloaded

perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene humandb/
perl annotate_variation.pl -buildver hg38 -downdb cytoBand humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar exac03 humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar avsnp147 humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar dbnsfp30a humandb/

[Ram]

This has already been answered 6 years ago. What value does your answer add? I'm moving it to a comment until you give some clarification on this.

Answer 1

[Kevin Blighe]

Yes, ANNOVAR supports hg38/GRCh38. You just have to install the databases by downloading them. Take a look here: http://annovar.openbioinformatics.org/en/latest/user-guide/startup/

For example:

annotate_variation.pl -buildver hg38 -downdb -webfrom annovar avsnp147 /Programs/ANNOVAR/database/humandb/

This will download dbSNP version 147 with hg38 co-ordinates to a directory called /Programs/ANNOVAR/database/humandb/. You can have multiple databases on your computer for each of hg18, hg19, and hg38.

When you then execute a further command to actually annotate variants make sure that you always use -buildver hg38 in the command, but you can flexibly use -buildver hg18 and -buildver hg19 if you have those installed too and also depending on the genome build of your data.

[Leandro Lima]

This also might be helpful: List all available databases for ANNOVAR

[Monisha]

I couldnot able to download these two datasets in ANNOVAR

perl annotate_variation.pl -buildver hg38 -downdb genomicSuperDups humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar snp138 humandb/

Is this is appropriate datasets for hg38? I'm newly using this ANNOVAR tool. PLEASE HELP!!