Question: New Variants Effect Prediction Tools
0
gravatar for cocchi.e89
4 months ago by
cocchi.e8930
cocchi.e8930 wrote:

Dear all, I am working on a database of several patients with relative variants (SNV and INDELS basically) VCF files. I know I can check for variant effect against VEP DB or similar, but for variants that are absent in such databases, how can I possibly categorize them in effect result? (e.g. missense vs nonsense etc)

Thanks a lot in advance for any help!

snv effect variant indel • 248 views
ADD COMMENTlink modified 4 months ago by Emily_Ensembl18k • written 4 months ago by cocchi.e8930
2

Pretty sure VEP will still tell you whether it's missense or nonsense even if it isn't a known variant. snpEff is another option that provides a wide breadth of output.

ADD REPLYlink written 4 months ago by jared.andrews072.8k

Thanks a lot for your reply! Do you know if they have downloadable DBs in to retrieve this information from? in order to automatized the annotation through a script?

ADD REPLYlink written 4 months ago by cocchi.e8930
2

http://snpeff.sourceforge.net/download.html#databases

ADD REPLYlink written 4 months ago by genomax70k
1
gravatar for Emily_Ensembl
4 months ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

The purpose of the VEP is to annotate variants with the effect the have on known genes. This works whether the variants are known (in which case extra information like frequency will also be provided) or novel. It's available as a web interface and an offline tool, all of which can be accessed here.

ADD COMMENTlink written 4 months ago by Emily_Ensembl18k

Thanks a lot! I red the info, so, if I download the caches I should find all infos even for unknown variants? Or you have to pass through VEP script anyway?

ADD REPLYlink written 4 months ago by cocchi.e8930

The caches aren't really human readable. They don't contain tinned information for every possible variant, they contain a bunch of data for the VEP to look up depending on what input you use. You should run your data through the VEP.

ADD REPLYlink written 4 months ago by Emily_Ensembl18k

Dear Emily, I tried to download and install the VEP app as suggested, but I encountered an error in downloading the cache and I can not work it out: you can see the error at the link: https://superuser.com/questions/1427147/mac-os-x-mojave-perl-5-xmldomxpath-test-non-ascii-fail

Do you have any suggestion to whom I should refer to in order to get help?

Thanks a lot in advance

ADD REPLYlink written 4 months ago by cocchi.e8930

Please can you send the error message, including at what stage of installing the VEP you got it, to helpdesk [at] ensembl.org.

ADD REPLYlink written 3 months ago by Emily_Ensembl18k

Dear Emily, I solved it out, the problem is that on the instruction page (https://useast.ensembl.org/info/docs/tools/vep/script/vep_download.html), "Installing BioPerl section" you recommend:

curl -O https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz
tar zxvf BioPerl-1.6.924.tar.gz
echo 'export PERL5LIB=${PERL5LIB}:##PATH_TO##/bioperl-1.6.924' >> ~/.bash_profile

but the names start with capital letters:

echo 'export PERL5LIB=${PERL5LIB}:##PATH_TO##/BioPerl-1.6.924' >> ~/.bash_profile

and it did not consider the right BioPerl version. Please point it out to webpage maintainers.

ADD REPLYlink modified 3 months ago • written 3 months ago by cocchi.e8930
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