Question: gene annotation with dbNSFP_gene
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gravatar for marta.rusmini
12 months ago by
marta.rusmini10 wrote:

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

next-gen gene • 476 views
ADD COMMENTlink modified 12 months ago by Kevin Blighe59k • written 12 months ago by marta.rusmini10

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

ADD REPLYlink written 4 months ago by Myosotis197910
0
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe59k
Kevin Blighe59k wrote:

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:

Kevin

ADD COMMENTlink written 12 months ago by Kevin Blighe59k

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?

ADD REPLYlink written 4 months ago by bernt.popp0

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.

To be honest, if you want to annotate your data with dbNSFP, just spend 1 day learning how to use ANNOVAR, which is much better, in my opinion. Downloading dbNSFP is also much easier and is automated.

ADD REPLYlink written 4 months ago by Kevin Blighe59k
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