[ensembl-dev] Annotations DBs

Wed Mar 11 10:34:23 GMT 2020

Hi Margaret,

The VEP cache files and the database both contain human SIFT and Polyphen data, so there should be no need to use this plugin. If you add the options '—sift b’ and/or ‘—polyphen b’ to your VEP command then you should receive the correct annotations (see https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_sift <https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_sift>) 

Regarding your connection issues to the ensembl database servers, are you able to successfully ping the ensembl servers with: 
ping -c 5 ensembldb.ensembl.org
If this ping is successful, then it may be that port 3306 is not open on your network.

Kind Regards,
Andrew

> On 10 Mar 2020, at 23:24, Linan, Margaret <margaret.linan at mssm.edu> wrote:
> 
> Hi- 
>  
> Where do I download the PolyPhen_SIFT.db file? I couldn’t create it either because there are problems connecting with the ensemble mysql db
>  
> DBI connect('host=ensembldb.ensembl.org <http://ensembldb.ensembl.org/>;port=3306','anonymous',...) failed: Unknown MySQL server host 'ensembldb.ensembl.org <http://ensembldb.ensembl.org/>' (11) at /home/margaret/Projects/ensembl-vep/Bio/EnsEMBL/Registry.pm line 1770.
>  
> -------------------- EXCEPTION --------------------
> MSG: Cannot connect to the Ensembl MySQL server at ensembldb.ensembl.org:3306 <http://ensembldb.ensembl.org:3306/>; check your settings & DBI error message: Unknown MySQL server host 'ensembldb.ensembl.org <http://ensembldb.ensembl.org/>' (11)
>  
> Here is documentation from the PolyPhen_SIFT plugin file.
> --------------------------------------------------------------------------------------------------------------------------
> A VEP plugin that retrieves PolyPhen and SIFT predictions from a
> locally constructed sqlite database. It can be used when your main
> source of VEP transcript annotation (e.g. a GFF file or GFF-based cache)
> does not contain these predictions.
>  
> You must either download or create a sqlite database of the predictions.
> You may point to the file by adding db=[file] as a parameter:
>  
> --plugin PolyPhen_SIFT,db=[file]
>  
> Human predictions (assembly-independent) are available here:
>  
> https://dl.dropboxusercontent.com/u/12936195/homo_sapiens.PolyPhen_SIFT.db <https://dl.dropboxusercontent.com/u/12936195/homo_sapiens.PolyPhen_SIFT.db>   ß Not available (no longer exists)
>  
> (Please note the download location of this file may change)
>  
> Place this file in $HOME/.vep to have the plugin find it automatically.
> You may change this directory by adding dir=[dir] as a parameter:
>  
> --plugin PolyPhen_SIFT,dir=[dir]
>  
> To create the database, you must have an active database connection
> (i.e. not using --offline) and add create_db=1 as a parameter:
>  
> --plugin PolyPhen_SIFT,create_db=1
> --------------------------------------------------------------------------------------------------------------------------
>  
> Best,
> Margaret
>  
> From: Dev <dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org>> On Behalf Of Andrew Parton
> Sent: Tuesday, March 10, 2020 3:41 AM
> To: Ensembl developers list <dev at ensembl.org <mailto:dev at ensembl.org>>
> Subject: Re: [ensembl-dev] Annotations DBs
>  
> USE CAUTION: External Message.
> Hi Margaret, 
>  
> VEP can provide annotations from three sources, which can be specified with a flag on VEP input:
>  
> —cache - Using a cache is the fastest and most efficient way to use VEP. With a cache file, the vast majority of annotations can be read from this file, reducing the number of required network connections. Cache files can be downloaded using the VEP installer, or can be downloaded manually if required. More information can be found on VEP caches here: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ensembl.org_info_docs_tools_vep_script_vep-5Fcache.html-23cache&d=DwMFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=kRxZpbitOhDkEC3BuUN1vDtzo3iicYrRn6woDJL_jnA&m=ckmCwWv2aOHlgURCqjAEFG3NRLLkGe81hdi6gjfQGrU&s=EuPq2OOXcTsL3ZaeT4NARRbtdvaGdc7t2pxc_bsPKDI&e=>
> —database - VEP can use remote or local database servers to retrieve annotations.  By default, VEP is configured to connect to the public Ensembl MySQL instance at ensembldb.ensembl.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__ensembldb.ensembl.org&d=DwMFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=kRxZpbitOhDkEC3BuUN1vDtzo3iicYrRn6woDJL_jnA&m=ckmCwWv2aOHlgURCqjAEFG3NRLLkGe81hdi6gjfQGrU&s=xxCjIHxXBnPLClgce83JrsJwTZQ2fnTClvIVM513DlA&e=>. You can find more information on how to access our database servers, or to set up a local database here: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#database <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ensembl.org_info_docs_tools_vep_script_vep-5Fcache.html-23database&d=DwMFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=kRxZpbitOhDkEC3BuUN1vDtzo3iicYrRn6woDJL_jnA&m=ckmCwWv2aOHlgURCqjAEFG3NRLLkGe81hdi6gjfQGrU&s=oHRqPFmEhohg1l7n6y2vmCf0U3GCfx_Lwl3bNUq207A&e=>
> —custom - If you have annotation data in a standard format such as GFF, VCF or BED, you can integrate this data into your VEP output using our custom annotation functionality. For more information on custom annotations, please see https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ensembl.org_info_docs_tools_vep_script_vep-5Fcustom.html&d=DwMFaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=kRxZpbitOhDkEC3BuUN1vDtzo3iicYrRn6woDJL_jnA&m=ckmCwWv2aOHlgURCqjAEFG3NRLLkGe81hdi6gjfQGrU&s=X15ABtkH0nI3mX9cr5MqzdVf8EcP4xdYXW9bhdHS1c4&e=>
>  
> Let us know if there’s anything else we can do to help.
>  
> Kind Regards,
> Andrew
>  
> On 10 Mar 2020, at 00:40, Linan, Margaret <margaret.linan at mssm.edu <mailto:margaret.linan at mssm.edu>> wrote:
>  
> Hi – 
>  
> How do you get the annotations dbs for VEP? I know I can specify them on the command line but they did not come with my installation.
>  
> Thanks,
> Margaret
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