Question: How to use GRCh38 as reference for Annotating the variants using Annovar?
2
gravatar for Karma
2.4 years ago by
Karma270
India
Karma270 wrote:

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?

next-gen annovar vcf • 2.1k views
ADD COMMENTlink modified 2.4 years ago by Kevin Blighe54k • written 2.4 years ago by Karma270
3
gravatar for Kevin Blighe
2.4 years ago by
Kevin Blighe54k
Kevin Blighe54k wrote:

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.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Kevin Blighe54k
1

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

ADD REPLYlink written 22 months ago by Leandro Lima930
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