Q: Why don't I see any co-located variations when using species X?
A: Ensembl only has variation databases for a subset of all Ensembl species - see this document for details.
Q: Why are some in/dels in my Pileup format file being given incorrect coordinates and/or allele string in the output?
A: This is a known issue with the Pileup parser - it is under investigation
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Q: How do I access the web version of the Variant Effect Predictor?
A: You can find the web VEP on the Tools page, or from any species-specific page by clicking the blue "Manage your data" link under the left-hand menu, then "Variant Effect Predictor".
Q: I have selected a VCF file in the file upload field, but nothing happens when I click the blue "Next" button. Why?
A: Ensure that you have selected VCF as the input file format, and that your VCF file is formatted correctly.
Q: I uploaded a file with 1000 variants, but some of them seem to be missing from the output?
A: Due to a limitation in the servers underlying Ensembl, only 750 variants in one file can be processed at once. Consider splitting your file into smaller chunks, or using the standalone perl script.
Q: Why is the output I get for my input file different when I use the web VEP and the VEP script?
A: Ensure that you are passing equivalent arguments to the script that you are using in the web version. If you are sure this is still a problem, please report it on the Ensembl developers mailing list, dev@ensembl.org.
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Q: Why do I see the following error?
Could not connect to database homo_sapiens_core_63_37 as user anonymous using [DBI:mysql:database=homo_sapiens_core_63_37;host=ensembldb.ensembl.org;port=5306] as a locator: Unknown MySQL server host 'ensembldb.ensembl.org' (2) at $HOME/src/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 290. -------------------- EXCEPTION -------------------- MSG: Could not connect to database homo_sapiens_core_63_37 as user anonymous using [DBI:mysql:database=homo_sapiens_core_63_37;host=ensembldb.ensembl.org;port=5306] as a locator: Unknown MySQL server host 'ensembldb.ensembl.org' (2)
A: By default the VEP script is configured to connect to the public MySQL server at ensembldb.ensembl.org. Occasionally the server may break connection with your script, which causes this error. This can happen when the server is busy, or due to various network issues. Consider using a local copy of the database, or the new caching system.
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