Vep download gtf file

The REST service does not return raw sequences, sample-haplotype assignments and the aligned sequences used to generate differences by default. The bioperl-ext package is no longer maintained and requires some tweaking to install. You may also need to edit the export command to point to the path created for the architecture on your machine. Skip to content. Star The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants www.

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To circumvent this you may provide VEP with a synonyms file. A synonym file is included in VEP's cache files, so if you have one of these for your species you can use it as follows:. VEP's flexibility does allow some annotation types to be replaced. The following table illustrates some examples and alternative means to retrieve equivalent data. By pointing VEP to a FASTA file or directory containing several files , it is possible to retrieve reference sequence locally when using --cache or --offline.

FASTA files can be set up using the installer ; files set up using the installer are automatically detected by VEP when using --cache or --offline ; you should not need to use --fasta to manually specify them.

See the Downloads page for details. You should preferably use the installer as described above to fetch these files; manual instructions are provided for reference.

An example set of commands for setting up the data for human follows:. To use the mirror, use the flag --host useastdb. Data for Ensembl Genomes species e. The appropriate connection parameters can be automatically loaded by using the flag --genomes.

If you have a very small data set s of variants , using the public database servers should provide adequate performance. If you have larger data sets, or wish to use VEP in a batch manner, consider one of the alternatives below. It is possible to set up a local MySQL mirror with the databases for your species of interest installed. For instructions on installing a local mirror, see here.

For most of the functionality of VEP, you will only need the Core database e. Follow us Blog Twitter. Personal Data. Arabidopsis thaliana. Oryza sativa Japonica Group. Physcomitrium patens. Actinidia chinensis.

Amborella trichopoda. Arabidopsis halleri. Asparagus officinalis. Brachypodium distachyon. Cannabis sativa female. Chlamydomonas reinhardtii. Corchorus capsularis. Cyanidioschyzon merolae. Dioscorea rotundata. Eutrema salsugineum. Galdieria sulphuraria. Gossypium raimondii.