gene annotation with dbNSFP_gene

Question

[marta.rusmini]

Hi Other then annotate the variants in my vcf, I would also like to annotate the genes. In particular, I'm interested in a brief description of the gene in order to have a primary indication to prioritize and filter variants. I used dbNSFP for variants annotation but I cannot understand how to anntate with the dataset dbNSFP_gene. Usually, for variants I used this script:

snpEff/SnpSift.jar dbnsfp -db dbNSFP3.5a_hg19_clean.txt.gz my.vcf> annotated.vcf

Which is the command for dbNSFP_gene?

Thank you very much

[Kevin Blighe]

Edit November 18, 2020 - this does not answer the question

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When you download the main dbNSFP file (>13GB), it should include a smaller file called dbNSFP[x.x]_gene, which is what you want to use. You will have to manually configure this for use with SnpSift. There are instructions here: 13. SnpSift dbNSFP. There, in the sub-section 'Building dbNSFP (for developers)', you'll be taken through an example of how you can prepare the _gene file for use.

Note that the _gene file can be directly downloaded from other sources:

• https://www.dnastar.com/blog/resources/dbnsfp-gene-level-annotations/

[bernt.popp]

Sorry Kevin, but your answer on biostars is either not up-to-date (maybe because the link you posted got updated) or does not answer this question. Can you please update your solution if you have one?

[Kevin Blighe]

Hey, to which link, specifically, are you referring? If you go to the first link and search for the header 'Building dbNSFP (for developers)', there are instructions there.

[kanika.151]

I think he is referring to this link: snpeff_dbnsfp

[Myosotis1979]

Hi Marta. Could you please tell me which are the commands/tools that you used to get your dbNFSP3.5a_hg19_clean.txt.gz database ? I'm not programmer and I struggled to annotate my VCF file for weeks :( .Thanks