Re: [vcfanno] Gene Annotation

[Brent Pedersen]

Hi Sugi, for gene annotation,
it's best to use a tool like snpEff or bcftools CSQ as those will also
give you the effect on each variant (missense/frameshift/synonymous
etc.).

If you really want to just annotate with gene, you can make a BED file
from UCSC.
-Brent

On Mon, May 10, 2021 at 4:08 PM Sugi Sivalingam
<s.siva...@uni-bonn.de> wrote:
>
>
> Dear Brent Pedersen,
>
> thank you for providing this great tool vcfanno. Could you recommend on the best source for gene annotation? There are so much sources out there like RefSeq, Ensembl and Gencode. What would you prefer do basic gene annotation of variants? Can you briefly provide the sources and how to prepare a gene annotation file for vcfanno?
>
> Many thanks in advance. Looking forward to hear from you soon.
>
> Best regards,
> SugiS
>
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