New Variants Effect Prediction Tools

Question

[cocchi.e89]

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!

[jared.andrews07]

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.

[cocchi.e89]

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?

[GenoMax]

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

Answer 1

[Emily]

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.

[cocchi.e89]

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?

[Emily]

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.

[cocchi.e89]

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

[Emily]

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

[cocchi.e89]

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.