Question: gene annotation with dbNSFP_gene
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gravatar for marta.rusmini
16 days ago by
marta.rusmini0 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 • 88 views
ADD COMMENTlink modified 13 days ago by Kevin Blighe42k • written 16 days ago by marta.rusmini0
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gravatar for Kevin Blighe
13 days ago by
Kevin Blighe42k
Kevin Blighe42k 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 13 days ago by Kevin Blighe42k
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