From 18518952236 at 163.com  Fri Oct 15 09:57:07 2021
From: 18518952236 at 163.com (=?utf-8?B?5b+D5Z+O?=)
Date: Fri, 15 Oct 2021 16:57:07 +0800
Subject: [ensembl-dev] =?utf-8?b?5Y2P5L2cIGphdmEgYXBp5byV5YWl?=
Message-ID: <8698488C-3F84-46B5-BD1E-9DC0B864E4CE@163.com>

???
  ????????Ensembl ???API ?? ??? human ???? rs7??????????????API??????Ensembl?? rs7 API???????????????????????
??????
??
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From 1738579862 at qq.com  Fri Oct 15 10:02:39 2021
From: 1738579862 at qq.com (=?gb18030?B?MTczODU3OTg2Mg==?=)
Date: Fri, 15 Oct 2021 17:02:39 +0800
Subject: [ensembl-dev] =?gb18030?b?u9i4tKO6INCt1/cgamF2YSBhcGnS/cjr?=
In-Reply-To: <8698488C-3F84-46B5-BD1E-9DC0B864E4CE@163.com>
References: <8698488C-3F84-46B5-BD1E-9DC0B864E4CE@163.com>
Message-ID: <tencent_AAA73CB41DF5FF612C1AE4552033E59C3E09@qq.com>

please see https://rest.ensembl.org/ ,you can find key




------------------&nbsp;????&nbsp;------------------
???:                                                                                                                        "Ensembl developers list"                                                                                    <18518952236 at 163.com&gt;;
????:&nbsp;2021?10?15?(???) ??4:57
???:&nbsp;"dev"<dev at ensembl.org&gt;;

??:&nbsp;[ensembl-dev] ?? java api??



???&nbsp; ????????Ensembl ???API ?? ??? human ???? rs7??????????????API??????Ensembl?? rs7 API???????????????????????
??????
??
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From danny.kunz at gmx.de  Fri Oct 15 10:27:28 2021
From: danny.kunz at gmx.de (danny.kunz at gmx.de)
Date: Fri, 15 Oct 2021 11:27:28 +0200
Subject: [ensembl-dev] 
	=?utf-8?b?5Zue5aSN77yaIOWNj+S9nCBqYXZhIGFwaeW8lQ==?=
	=?utf-8?b?5YWl?=
In-Reply-To: <tencent_AAA73CB41DF5FF612C1AE4552033E59C3E09@qq.com>
References: <8698488C-3F84-46B5-BD1E-9DC0B864E4CE@163.com>
 <tencent_AAA73CB41DF5FF612C1AE4552033E59C3E09@qq.com>
Message-ID: <005901d7c1a6$df5301d0$9df90570$@gmx.de>

There is an unofficial Github project available:

 

https://github.com/omnaest/Ensembl4J

 

Its only a smaller non regularly maintained sub project, which is part of our rare disease group projects, but it might work as a reference template for you as well.

 

Best regards,

Danny

 

-

 

???????Github?????

 

https://github.com/omnaest/Ensembl4J

 

???????????????????????????????????????????????????

 

??????

Danny

 

Von: Dev <dev-bounces at ensembl.org> Im Auftrag von 1738579862
Gesendet: Freitag, 15. Oktober 2021 11:03
An: Ensembl developers list <dev at ensembl.org>
Betreff: [ensembl-dev] ??? ?? java api??

 

please see https://rest.ensembl.org/ ,you can find key

 

 

------------------ ???? ------------------

???: "Ensembl developers list" < <mailto:18518952236 at 163.com> 18518952236 at 163.com>;

????: 2021?10?15?(???) ??4:57

???: "dev"< <mailto:dev at ensembl.org> dev at ensembl.org>;

??: [ensembl-dev] ?? java api??

 

???

  ????????Ensembl ???API ?? ??? human ???? rs7??????????????API??????Ensembl?? rs7 API???????????????????????

??????

??

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From 18518952236 at 163.com  Fri Oct 15 13:28:53 2021
From: 18518952236 at 163.com (=?utf-8?B?5b+D5Z+O?=)
Date: Fri, 15 Oct 2021 20:28:53 +0800
Subject: [ensembl-dev] 
 =?utf-8?b?5Zue5aSN77yaIOWNj+S9nCBqYXZhIGFwaeW8lQ==?=
 =?utf-8?b?5YWl?=
In-Reply-To: <005901d7c1a6$df5301d0$9df90570$@gmx.de>
References: <8698488C-3F84-46B5-BD1E-9DC0B864E4CE@163.com>
 <tencent_AAA73CB41DF5FF612C1AE4552033E59C3E09@qq.com>
 <005901d7c1a6$df5301d0$9df90570$@gmx.de>
Message-ID: <B33EE6D7-3127-4388-86A4-48D6B00233AF@163.com>

Ok 
Thanks for your help
I wish you a beautiful future
Thanks

> 2021?10?15? 17:27?danny.kunz at gmx.de ???
> 
> There is an unofficial Github project available:
>  
> https://github.com/omnaest/Ensembl4J <https://github.com/omnaest/Ensembl4J>
>  
> Its only a smaller non regularly maintained sub project, which is part of our rare disease group projects, but it might work as a reference template for you as well.
>  
> Best regards,
> Danny
>  
> -
>  
> ???????Github?????
>  
> https://github.com/omnaest/Ensembl4J <https://github.com/omnaest/Ensembl4J>
>  
> ???????????????????????????????????????????????????
>  
> ??????
> Danny
>  
> Von: Dev <dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org>> Im Auftrag von 1738579862
> Gesendet: Freitag, 15. Oktober 2021 11:03
> An: Ensembl developers list <dev at ensembl.org <mailto:dev at ensembl.org>>
> Betreff: [ensembl-dev] ??? ?? java api??
>  
> please see https://rest.ensembl.org/ <https://rest.ensembl.org/> ,you can find key
>  
>  
> ------------------ ???? ------------------
> ???: "Ensembl developers list" <18518952236 at 163.com <mailto:18518952236 at 163.com>>;
> ????: 2021?10?15?(???) ??4:57
> ???: "dev"<dev at ensembl.org <mailto:dev at ensembl.org>>;
> ??: [ensembl-dev] ?? java api??
>  
> ???
>   ????????Ensembl ???API ?? ??? human ???? rs7??????????????API??????Ensembl?? rs7 API???????????????????????
> ??????
> ??
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/

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From 18518952236 at 163.com  Tue Oct 19 02:46:53 2021
From: 18518952236 at 163.com (=?utf-8?B?5b+D5Z+O?=)
Date: Tue, 19 Oct 2021 09:46:53 +0800
Subject: [ensembl-dev] api
Message-ID: <A4BE867C-82B4-4A61-BEDD-9FBFC2536004@163.com>

Hello!
I tried http://rest.ensembl.org/variation/human/rs7? <http://rest.ensembl.org/variation/human/rs7?> Content type = Application / JSON interface
The data is returned, but the result I want is to jump to this page, so what should I do.
https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823
Best wishes
Thank you for your answer


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From 18518952236 at 163.com  Tue Oct 19 06:59:57 2021
From: 18518952236 at 163.com (=?utf-8?B?5b+D5Z+O?=)
Date: Tue, 19 Oct 2021 13:59:57 +0800
Subject: [ensembl-dev] 
 =?utf-8?b?5Zue5aSN77yaIOWNj+S9nCBqYXZhIGFwaeW8lQ==?=
 =?utf-8?b?5YWl?=
In-Reply-To: <005901d7c1a6$df5301d0$9df90570$@gmx.de>
References: <8698488C-3F84-46B5-BD1E-9DC0B864E4CE@163.com>
 <tencent_AAA73CB41DF5FF612C1AE4552033E59C3E09@qq.com>
 <005901d7c1a6$df5301d0$9df90570$@gmx.de>
Message-ID: <9D7B6BEF-381A-4A11-B83A-43D5DDEA76F3@163.com>

Hello!
I tried http://rest.ensembl.org/variation/human/rs7? <http://rest.ensembl.org/variation/human/rs7?> Content type = Application / JSON interface
The data is returned, but the result I want is to jump to this page, so what should I do.
https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823 <https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823>
Best wishes
Thank you for your answer


> 2021?10?15? 17:27?danny.kunz at gmx.de ???
> 
> There is an unofficial Github project available:
>  
> https://github.com/omnaest/Ensembl4J <https://github.com/omnaest/Ensembl4J>
>  
> Its only a smaller non regularly maintained sub project, which is part of our rare disease group projects, but it might work as a reference template for you as well.
>  
> Best regards,
> Danny
>  
> -
>  
> ???????Github?????
>  
> https://github.com/omnaest/Ensembl4J <https://github.com/omnaest/Ensembl4J>
>  
> ???????????????????????????????????????????????????
>  
> ??????
> Danny
>  
> Von: Dev <dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org>> Im Auftrag von 1738579862
> Gesendet: Freitag, 15. Oktober 2021 11:03
> An: Ensembl developers list <dev at ensembl.org <mailto:dev at ensembl.org>>
> Betreff: [ensembl-dev] ??? ?? java api??
>  
> please see https://rest.ensembl.org/ <https://rest.ensembl.org/> ,you can find key
>  
>  
> ------------------ ???? ------------------
> ???: "Ensembl developers list" <18518952236 at 163.com <mailto:18518952236 at 163.com>>;
> ????: 2021?10?15?(???) ??4:57
> ???: "dev"<dev at ensembl.org <mailto:dev at ensembl.org>>;
> ??: [ensembl-dev] ?? java api??
>  
> ???
>   ????????Ensembl ???API ?? ??? human ???? rs7??????????????API??????Ensembl?? rs7 API???????????????????????
> ??????
> ??
> _______________________________________________
> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org <https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org>
> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
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From sgiorgetti at ebi.ac.uk  Tue Oct 19 09:16:09 2021
From: sgiorgetti at ebi.ac.uk (Stefano Giorgetti)
Date: Tue, 19 Oct 2021 09:16:09 +0100
Subject: [ensembl-dev] 
 =?utf-8?b?5Zue5aSN77yaIOWNj+S9nCBqYXZhIGFwaeW8lQ==?=
 =?utf-8?b?5YWl?=
In-Reply-To: <9D7B6BEF-381A-4A11-B83A-43D5DDEA76F3@163.com>
References: <8698488C-3F84-46B5-BD1E-9DC0B864E4CE@163.com>
 <tencent_AAA73CB41DF5FF612C1AE4552033E59C3E09@qq.com>
 <005901d7c1a6$df5301d0$9df90570$@gmx.de>
 <9D7B6BEF-381A-4A11-B83A-43D5DDEA76F3@163.com>
Message-ID: <20211019081610.0845E62BA5D_16E7ECAB@hh-mx3.ebi.ac.uk>

Hello,

I am afraid I am not familiar with Ensembl4J project, but it looks like 
a (Java) wrapper to Ensembl REST.

If you want to have the information shown at 
https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823
<https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823>

available in Java, you can use the REST /variation_id/ and 
/variant_recorder/ endpoints. Please, find below links to the documentation

  * https://rest.ensembl.org/documentation/info/variation_id
  * https://rest.ensembl.org/documentation/info/variant_recoder

But if you truly want your application (web UI?) to display the page 
from Ensembl.org website, I think you should build the URL and redirect 
the user to it.
To build the URL, you might want to use the REST endpoints to get the 
information you need (chr, start, end positions in this case).

Hope it may help

Best wishes,
Stefano

On 19/10/2021 06:59, ?? wrote:
> Hello!
> I tried http://rest.ensembl.org/variation/human/rs7? 
> <http://rest.ensembl.org/variation/human/rs7?>?Content type = 
> Application / JSON interface
> The data is returned, but the result I want is to jump to this page, 
> so what should I do.
> https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823 
> <https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823>
> Best wishes
> Thank you for your answer
>
>
>> 2021?10?15? 17:27?danny.kunz at gmx.de <mailto:danny.kunz at gmx.de> ???
>>
>> There is an unofficial Github project available:
>> https://github.com/omnaest/Ensembl4J 
>> <https://github.com/omnaest/Ensembl4J>
>> Its only a smaller non regularly maintained sub project, which is 
>> part of our rare disease group projects, but it might work as a 
>> reference template for you as well.
>> Best regards,
>> Danny
>> -
>> ???????Github?????
>> https://github.com/omnaest/Ensembl4J 
>> <https://github.com/omnaest/Ensembl4J>
>> ???????????????????????????????????????????????????
>> ??????
>> Danny
>> *Von:*Dev <dev-bounces at ensembl.org 
>> <mailto:dev-bounces at ensembl.org>>*Im Auftrag von*1738579862
>> *Gesendet:*Freitag, 15.Oktober 2021 11:03
>> *An:*Ensembl developers list <dev at ensembl.org <mailto:dev at ensembl.org>>
>> *Betreff:*[ensembl-dev]?????java api??
>> please seehttps://rest.ensembl.org/ <https://rest.ensembl.org/>,you 
>> can find key
>> ------------------ ?????------------------
>> *???**:*"Ensembl developers list" <18518952236 at 163.com 
>> <mailto:18518952236 at 163.com>>;
>> *????**:*?2021?10?15?(???)??4:57
>> *???**:*?"dev"<dev at ensembl.org <mailto:dev at ensembl.org>>;
>> *?**?**:*?[ensembl-dev]??java api??
>> ???
>> ????????Ensembl???API?????human????rs7??????????????API??????Ensembl??rs7 
>> API???????????????????????
>> ??????
>> ??
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe 
>> info:https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org 
>> <https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org>
>> Ensembl Blog:http://www.ensembl.info/ <http://www.ensembl.info/>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
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From emily at ebi.ac.uk  Tue Oct 19 09:21:10 2021
From: emily at ebi.ac.uk (Emily Perry)
Date: Tue, 19 Oct 2021 09:21:10 +0100
Subject: [ensembl-dev] api
In-Reply-To: <20211019014849.3798E119EAC_16E2401B@hh-mx4.ebi.ac.uk>
References: <20211019014849.3798E119EAC_16E2401B@hh-mx4.ebi.ac.uk>
Message-ID: <0E4BE9E9-0263-4F6E-A568-133D26A552F3@ebi.ac.uk>

Hello

To jump to the page just use https://asia.ensembl.org/Homo_sapiens/Variation/Explore?v=rs7 <https://asia.ensembl.org/Homo_sapiens/Variation/Explore?v=rs7>

All the best

Emily

> On 19 Oct 2021, at 02:46, ?? <18518952236 at 163.com> wrote:
> 
> Hello!
> I tried http://rest.ensembl.org/variation/human/rs7? <http://rest.ensembl.org/variation/human/rs7?> Content type = Application / JSON interface
> The data is returned, but the result I want is to jump to this page, so what should I do.
> https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823 <https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823>
> Best wishes
> Thank you for your answer
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/

?

Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader 
(she/her)

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory 
Wellcome Genome Campus
Hinxton
Cambridge
CB10 1SD
UK 




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From 18518952236 at 163.com  Tue Oct 19 11:31:51 2021
From: 18518952236 at 163.com (=?utf-8?B?5b+D5Z+O?=)
Date: Tue, 19 Oct 2021 18:31:51 +0800
Subject: [ensembl-dev] api
In-Reply-To: <0E4BE9E9-0263-4F6E-A568-133D26A552F3@ebi.ac.uk>
References: <20211019014849.3798E119EAC_16E2401B@hh-mx4.ebi.ac.uk>
 <0E4BE9E9-0263-4F6E-A568-133D26A552F3@ebi.ac.uk>
Message-ID: <8CB72928-3D75-431A-A1B5-D3AA46605D61@163.com>

Thank you for solving my problem
I wish you a beautiful day


> 2021?10?19? 16:21?Emily Perry <emily at ebi.ac.uk> ???
> 
> Hello
> 
> To jump to the page just use https://asia.ensembl.org/Homo_sapiens/Variation/Explore?v=rs7 <https://asia.ensembl.org/Homo_sapiens/Variation/Explore?v=rs7>
> 
> All the best
> 
> Emily
> 
>> On 19 Oct 2021, at 02:46, ?? <18518952236 at 163.com <mailto:18518952236 at 163.com>> wrote:
>> 
>> Hello!
>> I tried http://rest.ensembl.org/variation/human/rs7? <http://rest.ensembl.org/variation/human/rs7?> Content type = Application / JSON interface
>> The data is returned, but the result I want is to jump to this page, so what should I do.
>> https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823 <https://asia.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:92149743-92150743;v=rs7;vdb=variation;vf=728758823>
>> Best wishes
>> Thank you for your answer
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org <https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org>
>> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
> 
> ?
> 
> Dr Emily Perry (Pritchard)
> Ensembl Outreach Project Leader 
> (she/her)
> 
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory 
> Wellcome Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> UK 
> 
> 
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/

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From alexei_podtelezhnikov at merck.com  Thu Oct 21 22:19:34 2021
From: alexei_podtelezhnikov at merck.com (Podtelezhnikov, Alexei)
Date: Thu, 21 Oct 2021 21:19:34 +0000
Subject: [ensembl-dev] Ugt1a locus in rat
Message-ID: <DM6P106MB0280BADDBBE54E5B0BB562C280BF9@DM6P106MB0280.NAMP106.PROD.OUTLOOK.COM>

Dear developers,

The tox community looks forward to the mRatBN7.2 assembly that should come in Ensembl 105. My benchmark is Ugt1a locus (ENSRNOG00000018740) which is historically very problematic for Ensembl. Mouse and Human get it right with multiple genes having distant first exons (and promoters) but sharing the trailing exons. Rat was never correct when using transcript variants of a single gene. What is even more confusing that the rat gene name is randomly changing: Ugt1a3 in Rapid, Ugt1a6 in 104, Ugt1a3 in 96, Ugt1a5 in 90, and so on.

In general the Rapid with mRatBN7.2 is much improved with fewer gene duplications and less gene entanglement in large families. It is just Ugt1a family which continues to be a problem. I suggest that this family be aligned with NCBI and with mouse and human. I think there should be reasonable alignment between three mammalian genomes selected for GRC.

Please consider this improvement for the future release. Thank you for your time and help.

Alexei

Alexei A Podtelezhnikov, PhD
Principal Scientist
Genome & Biomarker Sciences
Merck & Co., Inc.

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From myourshaw at gmail.com  Fri Oct 22 22:30:12 2021
From: myourshaw at gmail.com (Michael Yourshaw)
Date: Fri, 22 Oct 2021 15:30:12 -0600
Subject: [ensembl-dev] missing some used_ref fields in VEP json output
Message-ID: <CANcs_JJU+Q_ssNiPcMC1AHsCx3pVvCVw2WX_AD_1VpU-hiuhJQ@mail.gmail.com>

When I updated to the latest VEP I encountered a handful of transcripts in
the json output that did not contain a used_ref field. This seems to be a
problem introduced recently and does not affect the great majority of
variants.

An example record:

is attached.


?
Michael Yourshaw
myourshaw at gmail.com <myourshaw at ucla.edu>

This message is intended only for the use of the addressee and may contain
information that is PRIVILEGED and CONFIDENTIAL, and/or may contain
ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are
hereby notified that any dissemination of this communication is strictly
prohibited. If you have received this communication in error, please erase
all copies of the message and its attachments and notify us immediately.
Thank you.
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From dlemos at ebi.ac.uk  Tue Oct 26 15:12:48 2021
From: dlemos at ebi.ac.uk (Diana Lemos)
Date: Tue, 26 Oct 2021 15:12:48 +0100
Subject: [ensembl-dev] missing some used_ref fields in VEP json output
In-Reply-To: <20211022213236.3DCD162CEF1_1732DF4B@hh-mx3.ebi.ac.uk>
References: <20211022213236.3DCD162CEF1_1732DF4B@hh-mx3.ebi.ac.uk>
Message-ID: <b50b7557-e4aa-23f2-fe39-3eefc58196a7@ebi.ac.uk>

Hi Michael,

Thank you for reporting this issue.

The JSON output does not include used_ref and given_ref if the ref is 
"-" which is the case for your example. We are working on a fix.


Best wishes,

Diana


On 22/10/2021 22:30, Michael Yourshaw wrote:
> When I updated to the latest VEP I encountered a handful of 
> transcripts in the json output that did not contain a used_ref field. 
> This seems to be a problem introduced recently and does not affect the 
> great majority of variants.
>
> An example record:
>
> is attached.
>
>
> ?
> Michael Yourshaw
> myourshaw at gmail.com <mailto:myourshaw at ucla.edu>
>
> This message is intended only for the use of the addressee and may 
> contain information that is PRIVILEGED and CONFIDENTIAL, and/or may 
> contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, 
> you are hereby notified that any dissemination of this communication 
> is strictly prohibited. If you have received this communication in 
> error, please erase all copies of the message and its attachments and 
> notify us immediately. Thank you.
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
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From hpages.on.github at gmail.com  Tue Oct 26 22:55:45 2021
From: hpages.on.github at gmail.com (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Tue, 26 Oct 2021 14:55:45 -0700
Subject: [ensembl-dev] Transcripts missing in Mus_musculus.GRCm38.102.gtf.gz
 and Mus_musculus.GRCm38.102.gff3.gz
Message-ID: <6dece495-c90d-4701-1267-dfd29d72443c@gmail.com>

Hi,

Does anybody know why transcript ENSMUST00000230762 is missing from the 
GTF and GFF3 files for Mus musculus in Ensembl release 102?

ENSMUST00000230762 is a transcript present in the 
mus_musculus_core_102_38 db. It's located on novel-patch sequence 
CHR_WSB_EIJ_MMCHR11_CTG3 from GRCm38.p6. But for some reason it's not in 
the Mus_musculus.GRCm38.102.gtf.gz or Mus_musculus.GRCm38.102.gff3.gz 
files found here 
http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/ and here 
http://ftp.ensembl.org/pub/release-102/gff3/mus_musculus/

Furthermore, it seems that the GTF and GTF3 files are missing 2079 
transcripts compared to the mus_musculus_core_102_38 db. Anybody knows 
what's going on?

Thanks,
H.

-- 
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com



From tdanhorn at gmail.com  Wed Oct 27 00:22:21 2021
From: tdanhorn at gmail.com (Thomas Danhorn)
Date: Tue, 26 Oct 2021 17:22:21 -0600 (MDT)
Subject: [ensembl-dev] Transcripts missing in
 Mus_musculus.GRCm38.102.gtf.gz and Mus_musculus.GRCm38.102.gff3.gz
In-Reply-To: <6dece495-c90d-4701-1267-dfd29d72443c@gmail.com>
References: <6dece495-c90d-4701-1267-dfd29d72443c@gmail.com>
Message-ID: <36387da-6a6-4d7-9c77-915614098d0@gmail.com>

As far as I know, these GTFs/GFFs only contain genes and transcripts from 
the primary assembly, i.e. not from patches.  I suspect 
http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.chr_patch_hapl_scaff.gtf.gz
might contain such transcripts.

Best wishes,

Thomas


On Tue, 26 Oct 2021, Herv? Pag?s wrote:

> Hi,
>
> Does anybody know why transcript ENSMUST00000230762 is missing from the 
> GTF and GFF3 files for Mus musculus in Ensembl release 102?
>
> ENSMUST00000230762 is a transcript present in the 
> mus_musculus_core_102_38 db. It's located on novel-patch sequence 
> CHR_WSB_EIJ_MMCHR11_CTG3 from GRCm38.p6. But for some reason it's not in 
> the Mus_musculus.GRCm38.102.gtf.gz or Mus_musculus.GRCm38.102.gff3.gz 
> files found here 
> http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/ and here 
> http://ftp.ensembl.org/pub/release-102/gff3/mus_musculus/
>
> Furthermore, it seems that the GTF and GTF3 files are missing 2079 
> transcripts compared to the mus_musculus_core_102_38 db. Anybody knows 
> what's going on?
>
> Thanks,
> H.
>
> -- 
> Herv? Pag?s
>
> Bioconductor Core Team
> hpages.on.github at gmail.com
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: 
> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
>

From hpages.on.github at gmail.com  Wed Oct 27 00:37:14 2021
From: hpages.on.github at gmail.com (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Tue, 26 Oct 2021 16:37:14 -0700
Subject: [ensembl-dev] Transcripts missing in
 Mus_musculus.GRCm38.102.gtf.gz and Mus_musculus.GRCm38.102.gff3.gz
In-Reply-To: <36387da-6a6-4d7-9c77-915614098d0@gmail.com>
References: <6dece495-c90d-4701-1267-dfd29d72443c@gmail.com>
 <36387da-6a6-4d7-9c77-915614098d0@gmail.com>
Message-ID: <6cfcfc96-594e-87ea-1fb0-d6684b9d1e87@gmail.com>

That's it. These *.chr_patch_hapl_scaff.* files seem indeed to contain 
the full db dump. Thanks!

Cheers,
H.


On 26/10/2021 16:22, Thomas Danhorn wrote:
> As far as I know, these GTFs/GFFs only contain genes and transcripts 
> from the primary assembly, i.e. not from patches.? I suspect 
> http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.chr_patch_hapl_scaff.gtf.gz 
> 
> might contain such transcripts.
> 
> Best wishes,
> 
> Thomas
> 
> 
> On Tue, 26 Oct 2021, Herv? Pag?s wrote:
> 
>> Hi,
>>
>> Does anybody know why transcript ENSMUST00000230762 is missing from 
>> the GTF and GFF3 files for Mus musculus in Ensembl release 102?
>>
>> ENSMUST00000230762 is a transcript present in the 
>> mus_musculus_core_102_38 db. It's located on novel-patch sequence 
>> CHR_WSB_EIJ_MMCHR11_CTG3 from GRCm38.p6. But for some reason it's not 
>> in the Mus_musculus.GRCm38.102.gtf.gz or 
>> Mus_musculus.GRCm38.102.gff3.gz files found here 
>> http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/ and here 
>> http://ftp.ensembl.org/pub/release-102/gff3/mus_musculus/
>>
>> Furthermore, it seems that the GTF and GTF3 files are missing 2079 
>> transcripts compared to the mus_musculus_core_102_38 db. Anybody knows 
>> what's going on?
>>
>> Thanks,
>> H.
>>
>> -- 
>> Herv? Pag?s
>>
>> Bioconductor Core Team
>> hpages.on.github at gmail.com
>>
>> _______________________________________________
>> Dev mailing list??? Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: 
>> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
>> Ensembl Blog: http://www.ensembl.info/
>>
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
> 

-- 
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com



From hpages.on.github at gmail.com  Wed Oct 27 00:54:34 2021
From: hpages.on.github at gmail.com (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Tue, 26 Oct 2021 16:54:34 -0700
Subject: [ensembl-dev] Transcripts missing in
 Mus_musculus.GRCm38.102.gtf.gz and Mus_musculus.GRCm38.102.gff3.gz
In-Reply-To: <6cfcfc96-594e-87ea-1fb0-d6684b9d1e87@gmail.com>
References: <6dece495-c90d-4701-1267-dfd29d72443c@gmail.com>
 <36387da-6a6-4d7-9c77-915614098d0@gmail.com>
 <6cfcfc96-594e-87ea-1fb0-d6684b9d1e87@gmail.com>
Message-ID: <bd1c69b3-c3db-34c0-dd07-bf56a04cea66@gmail.com>

Hmm.. not quite. GFF3 file 
Mus_musculus.GRCm38.102.chr_patch_hapl_scaff.gff3.gz still seems to be 
missing some transcripts.

The mus_musculus_core_102_38 db and 
Mus_musculus.GRCm38.102.chr_patch_hapl_scaff.gtf.gz both contain 144778 
transcripts but Mus_musculus.GRCm38.102.chr_patch_hapl_scaff.gff3.gz 
contains only 144726. So 52 transcripts are missing. For example 
ENSMUST00000206994 is missing. This transcript belongs to gene 
ENSMUSG00000108408. So this gene has 5 transcripts in the GTF file but 
only 4 in the GFF3 file.

What could be the reason why some transcripts are excluded from the GFF3 
file?

Thanks,
H.


On 26/10/2021 16:37, Herv? Pag?s wrote:
> That's it. These *.chr_patch_hapl_scaff.* files seem indeed to contain 
> the full db dump. Thanks!
> 
> Cheers,
> H.
> 
> 
> On 26/10/2021 16:22, Thomas Danhorn wrote:
>> As far as I know, these GTFs/GFFs only contain genes and transcripts 
>> from the primary assembly, i.e. not from patches.? I suspect 
>> http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.chr_patch_hapl_scaff.gtf.gz 
>>
>> might contain such transcripts.
>>
>> Best wishes,
>>
>> Thomas
>>
>>
>> On Tue, 26 Oct 2021, Herv? Pag?s wrote:
>>
>>> Hi,
>>>
>>> Does anybody know why transcript ENSMUST00000230762 is missing from 
>>> the GTF and GFF3 files for Mus musculus in Ensembl release 102?
>>>
>>> ENSMUST00000230762 is a transcript present in the 
>>> mus_musculus_core_102_38 db. It's located on novel-patch sequence 
>>> CHR_WSB_EIJ_MMCHR11_CTG3 from GRCm38.p6. But for some reason it's not 
>>> in the Mus_musculus.GRCm38.102.gtf.gz or 
>>> Mus_musculus.GRCm38.102.gff3.gz files found here 
>>> http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/ and here 
>>> http://ftp.ensembl.org/pub/release-102/gff3/mus_musculus/
>>>
>>> Furthermore, it seems that the GTF and GTF3 files are missing 2079 
>>> transcripts compared to the mus_musculus_core_102_38 db. Anybody 
>>> knows what's going on?
>>>
>>> Thanks,
>>> H.
>>>
>>> -- 
>>> Herv? Pag?s
>>>
>>> Bioconductor Core Team
>>> hpages.on.github at gmail.com
>>>
>>> _______________________________________________
>>> Dev mailing list??? Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info: 
>>> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>
>> _______________________________________________
>> Dev mailing list??? Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: 
>> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
>> Ensembl Blog: http://www.ensembl.info/
>>
> 

-- 
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com



From amandine.septier at univ-grenoble-alpes.fr  Thu Oct 28 08:44:25 2021
From: amandine.septier at univ-grenoble-alpes.fr (AMANDINE SEPTIER)
Date: Thu, 28 Oct 2021 09:44:25 +0200 (CEST)
Subject: [ensembl-dev] CNV IMPACT
Message-ID: <768093196.26437336.1635407065058.JavaMail.zimbra@univ-grenoble-alpes.fr>

Hello VEP team, 

Thank you very much for your tool. 
I send you this mail because I'm analyzing Exome data and making CNV calls on a patients cohort. 
When I annotate SVs with VEP, it returns "MODIFIER" hits for CNVs covering several exons/introns without covering the entire impacted gene(s).(details below) 
Some of them are experimentally validated, so it is a pity that VEP doesn't send back these CNVs. (ex : CFAP251) 
Is it possible to put more weight on the 'feature_truncation' or 'feature_elongation' variants consequences so that they have a greater impact? 
This is just a discussion I'm opening up. 
Thanks in advance for your future return. 
Regards. 
-- 
---------------------------------------------------------------------- 
Amandine SEPTIER 
Doctorante 
Laboratoire TIMC-IMAG/MAGe, CNRS UMR 5525 
Pavillon Taillefer, Facult? de M?decine 
38700 La Tronche, France 
--------------------------------------------------------------- 

VCF INPUT: 
##fileformat=VCFv4.3 
##fileDate=20211027 
##ALT=<ID=DEL,Description="Deletion"> 
##ALT=<ID=DUP,Description="Duplication"> 
##ALT=<ID=CNV,Description="Copy number variable region"> 
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> 
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> 
##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype"> 
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events"> 
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 
[ callto:4 146867498 | 4??? 146867498 ] TTC29_HetDEL . <DEL> . . SVTYPE=DEL;END=146867583 GT:CN 0/1:1 ./.:2 ./.:2 
[ callto:12 121908103 | 12??? 121908103 ] CFAP251_AllGene . <DEL> . . SVTYPE=DEL;END=122003919 GT:CN 1/1:0 1/1:0 1/1:0 
[ callto:12 121999716 | 12??? 121999716 ] CFAP251_HomoDEL . <DEL> . . SVTYPE=DEL;END=122001598 GT:CN 1/1:0 1/1:0 1/1:0 
[ callto:12 121999716 | 12??? 121999716 ] CFAP251_exon20/22 . <DEL> . . SVTYPE=DEL;END=121999944 GT:CN 1/1:0 1/1:0 1/1:0 
[ callto:12 122001497 | 12??? 122001497 ] CFAP251_exon21/22 . <DEL> . . SVTYPE=DEL;END=122001598 GT:CN 1/1:0 1/1:0 1/1:0 

COMMAND LINE: 
vep -i VEPtest_211027.vcf --cache --offline --force_overwrite --format vcf --vcf -o OutVEP_211027.csv 

OUTPUT 
##fileformat=VCFv4.3 
##fileDate=20211027 
##ALT=<ID=DEL,Description="Deletion"> 
##ALT=<ID=DUP,Description="Duplication"> 
##ALT=<ID=CNV,Description="Copy number variable region"> 
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> 
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> 
##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype"> 
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events"> 
##VEP="v104" time=" [ callto:2021-10-27 11 | 2021-10-27 11 ] :56:04" cache="/home/septiera/.vep/homo_sapiens/104_GRCh38" ensembl-funcgen=104.59ae779 ensembl-variation=104.6154f8b ensembl=104.1af1dce ensembl-io=104.1d3bb6e 1000genomes="phase3" COSMIC="92" ClinVar="20210102" ESP="V2-SSA137" HGMD-PUBLIC="20204" assembly="GRCh38.p13" dbSNP="154" gencode="GENCODE 38" genebuild="2014-07" gnomAD="r2.1.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2" 
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID"> 
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 
[ callto:4 146867498 | 4??? 146867498 ] TTC29_HetDEL . <DEL> . . SVTYPE=DEL;END=146867583;CSQ=deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000325106|protein_coding|8/13||||1009-1093|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000504425|protein_coding|8/13||||1027-1111|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&NMD_transcript_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000508306|nonsense_mediated_decay|8/14||||978-1062|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000513335|protein_coding|9/14||||1078-1162|878-962|293-321|||||-1||HGNC|HGNC:29936 GT:CN 0/1:1 ./.:2 ./.:2 
[ callto:12 121908103 | 12??? 121908103 ] CFAP251_AllGene . <DEL> . . SVTYPE=DEL;END=122003919;CSQ=deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000261817|protein_coding|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding||||||||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000361485|retained_intron||||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000397454|protein_coding||||||||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|RNU7-170P|ENSG00000239082|Transcript|ENST00000459303|snRNA|1/1||||2-?|||||||1||HGNC|HGNC:45704,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000535257|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000535293|nonsense_mediated_decay|4-5/5|3-4/4||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000537407|nonsense_mediated_decay|5-7/7|4-6/6||||||||||1||HGNC|HGNC:9567,deletion|downstream_gene_variant|MODIFIER||ENSG00000255856|Transcript|ENST00000538710|lncRNA|||||||||||3515|-1|||,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000540779|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000540962|nonsense_mediated_decay|4-5/5|3-4/4||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000541212|protein_coding|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000542602|protein_coding|3-4/4|2-3/3||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000543211|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000543699|nonsense_mediated_decay|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000544254|retained_intron|2-3/3|1-2/2||||||||||1||HGNC|HGNC:9567,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000544724|retained_intron|3-4/4|2-3/3||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH||ENSG00000256950|Transcript|ENST00000544911|retained_intron||||||||||||1|||,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000545752|processed_transcript||||||||||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|1-2/2|1/1|||?-484|||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000546044|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER||ENSG00000256950|Transcript|ENST00000546333|nonsense_mediated_decay|4/4|3/3||||||||||1||| GT:CN 1/1:0 1/1:0 1/1:0 
[ callto:12 121999716 | 12??? 121999716 ] CFAP251_HomoDEL . <DEL> . . SVTYPE=DEL;END=122001598;CSQ=deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|20-21/22|20/21|||3132-3461|3008-3337|1003-1113|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|1-2/3|1/2|||2832-3161|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||106|1||HGNC|HGNC:28506 GT:CN 1/1:0 1/1:0 1/1:0 
[ callto:12 121999716 | 12??? 121999716 ] CFAP251_Corrpad_exon20/22 . <DEL> . . SVTYPE=DEL;END=121999944;CSQ=deletion|inframe_deletion&feature_truncation|MODERATE|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|20/22||||3132-3359|3008-3235|1003-1079|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|1/3||||2832-3059|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||1760|1||HGNC|HGNC:28506 GT:CN 1/1:0 1/1:0 1/1:0 
[ callto:12 122001497 | 12??? 122001497 ] CFAP251_Corrpad_exon21/22 . <DEL> . . SVTYPE=DEL;END=122001598;CSQ=deletion|frameshift_variant&feature_truncation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|21/22||||3361-3461|3237-3337|1079-1113|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|2/3||||3061-3161|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||106|1||HGNC|HGNC:28506 GT:CN 1/1:0 1/1:0 1/1:0 

System 


    * VEP version: 104.3 
    * VEP Cache version: homo_sapiens_vep_104_GRCh38 
    * Perl version: perl-5.16.3-299.el7_9.x86_64 
    * OS: centos 7 
    * tabix installed ? yes 

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From dlemos at ebi.ac.uk  Thu Oct 28 13:38:49 2021
From: dlemos at ebi.ac.uk (Diana Lemos)
Date: Thu, 28 Oct 2021 13:38:49 +0100
Subject: [ensembl-dev] CNV IMPACT
In-Reply-To: <20211028074636.71A5762A233_17A555CB@hh-mx3.ebi.ac.uk>
References: <20211028074636.71A5762A233_17A555CB@hh-mx3.ebi.ac.uk>
Message-ID: <469fbc6e-d736-18a0-39cd-11003dcda5aa@ebi.ac.uk>

Hi Amandine,

The IMPACT column is a subjective classification of the severity of the 
variant consequence. It is a separate rating given for compatibility 
with other variant annotation tools e.g. snpEff. As this rating is 
subjective, you can always get the full set of consequences for each 
allele and make your own severity judgement.

Information on all of our consequences can be found here: 
https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html 
<https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html>


Best wishes,

Diana


On 28/10/2021 08:44, AMANDINE SEPTIER wrote:
> Hello VEP team,
>
> Thank you very much for your tool.
> I send you this mail because I'm analyzing Exome data and making CNV 
> calls on a patients cohort.
> When I annotate SVs with VEP, it returns "MODIFIER" hits for CNVs 
> covering several exons/introns without covering the entire impacted 
> gene(s).(details below)
> Some of them are experimentally validated, so it is a pity that VEP 
> doesn't send back these CNVs. (ex : CFAP251)
> Is it possible to put more weight on the 'feature_truncation' or 
> 'feature_elongation' variants consequences so that they have a greater 
> impact?
> This is just a discussion I'm opening up.
> Thanks in advance for your future return.
> Regards.
> -- 
> ----------------------------------------------------------------------
> Amandine SEPTIER
> Doctorante
> Laboratoire TIMC-IMAG/MAGe, CNRS UMR 5525
> Pavillon Taillefer, Facult? de M?decine
> 38700 La Tronche, France
> ---------------------------------------------------------------
>
> VCF INPUT:
> ##fileformat=VCFv4.3
> ##fileDate=20211027
> ##ALT=<ID=DEL,Description="Deletion">
> ##ALT=<ID=DUP,Description="Duplication">
> ##ALT=<ID=CNV,Description="Copy number variable region">
> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural 
> variant">
> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the 
> variant described in this record">
> ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
> ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number 
> genotype for imprecise events">
> #CHROM??? POS??? ID??? REF??? ALT??? QUAL FILTER??? INFO??? FORMAT??? 
> S1??? S2??? S3
> 4??? 146867498 <callto:4 146867498> TTC29_HetDEL??? .??? <DEL>??? .??? 
> . SVTYPE=DEL;END=146867583??? GT:CN??? 0/1:1 ./.:2??? ./.:2
> 12??? 121908103 <callto:12 121908103> CFAP251_AllGene??? .??? <DEL>??? 
> .??? . SVTYPE=DEL;END=122003919??? GT:CN??? 1/1:0 1/1:0??? 1/1:0
> 12??? 121999716 <callto:12 121999716> CFAP251_HomoDEL??? .??? <DEL>??? 
> .??? . SVTYPE=DEL;END=122001598??? GT:CN??? 1/1:0 1/1:0??? 1/1:0
> 12??? 121999716 <callto:12 121999716> CFAP251_exon20/22??? .??? 
> <DEL>??? .??? . SVTYPE=DEL;END=121999944??? GT:CN??? 1/1:0 1/1:0??? 1/1:0
> 12??? 122001497 <callto:12 122001497> CFAP251_exon21/22??? .??? 
> <DEL>??? .??? . SVTYPE=DEL;END=122001598??? GT:CN??? 1/1:0 1/1:0??? 1/1:0
>
> COMMAND LINE:
> vep -i VEPtest_211027.vcf --cache --offline --force_overwrite --format 
> vcf --vcf -o OutVEP_211027.csv
>
> OUTPUT
> ##fileformat=VCFv4.3
> ##fileDate=20211027
> ##ALT=<ID=DEL,Description="Deletion">
> ##ALT=<ID=DUP,Description="Duplication">
> ##ALT=<ID=CNV,Description="Copy number variable region">
> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural 
> variant">
> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the 
> variant described in this record">
> ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
> ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number 
> genotype for imprecise events">
> ##VEP="v104" time="2021-10-27 11 <callto:2021-10-27 11>:56:04" 
> cache="/home/septiera/.vep/homo_sapiens/104_GRCh38" 
> ensembl-funcgen=104.59ae779 ensembl-variation=104.6154f8b 
> ensembl=104.1af1dce ensembl-io=104.1d3bb6e 1000genomes="phase3" 
> COSMIC="92" ClinVar="20210102" ESP="V2-SSA137" HGMD-PUBLIC="20204" 
> assembly="GRCh38.p13" dbSNP="154" gencode="GENCODE 38" 
> genebuild="2014-07" gnomAD="r2.1.1" polyphen="2.2.2" regbuild="1.0" 
> sift="sift5.2.2"
> ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence 
> annotations from Ensembl VEP. Format: 
> Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID">
> #CHROM??? POS??? ID??? REF??? ALT??? QUAL FILTER??? INFO??? FORMAT??? 
> S1??? S2??? S3
> 4??? 146867498 <callto:4 146867498> TTC29_HetDEL??? .??? <DEL>??? .??? 
> . 
> SVTYPE=DEL;END=146867583;CSQ=deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000325106|protein_coding|8/13||||1009-1093|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000504425|protein_coding|8/13||||1027-1111|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&NMD_transcript_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000508306|nonsense_mediated_decay|8/14||||978-1062|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000513335|protein_coding|9/14||||1078-1162|878-962|293-321|||||-1||HGNC|HGNC:29936 
> GT:CN??? 0/1:1??? ./.:2??? ./.:2
> 12??? 121908103 <callto:12 121908103> CFAP251_AllGene??? .??? <DEL>??? 
> .??? . 
> SVTYPE=DEL;END=122003919;CSQ=deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000261817|protein_coding|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding||||||||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000361485|retained_intron||||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000397454|protein_coding||||||||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|RNU7-170P|ENSG00000239082|Transcript|ENST00000459303|snRNA|1/1||||2-?|||||||1||HGNC|HGNC:45704,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000535257|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000535293|nonsense_mediated_decay|4-5/5|3-4/4||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000537407|nonsense_mediated_decay|5-7/7|4-6/6||||||||||1||HGNC|HGNC:9567,deletion|downstream_gene_variant|MODIFIER||ENSG00000255856|Transcript|ENST00000538710|lncRNA|||||||||||3515|-1|||,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000540779|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000540962|nonsense_mediated_decay|4-5/5|3-4/4||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000541212|protein_coding|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000542602|protein_coding|3-4/4|2-3/3||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000543211|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000543699|nonsense_mediated_decay|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000544254|retained_intron|2-3/3|1-2/2||||||||||1||HGNC|HGNC:9567,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000544724|retained_intron|3-4/4|2-3/3||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH||ENSG00000256950|Transcript|ENST00000544911|retained_intron||||||||||||1|||,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000545752|processed_transcript||||||||||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|1-2/2|1/1|||?-484|||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000546044|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER||ENSG00000256950|Transcript|ENST00000546333|nonsense_mediated_decay|4/4|3/3||||||||||1||| 
> GT:CN??? 1/1:0??? 1/1:0??? 1/1:0
> 12??? 121999716 <callto:12 121999716> CFAP251_HomoDEL??? .??? <DEL>??? 
> .??? . 
> SVTYPE=DEL;END=122001598;CSQ=deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|20-21/22|20/21|||3132-3461|3008-3337|1003-1113|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|1-2/3|1/2|||2832-3161|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||106|1||HGNC|HGNC:28506 
> GT:CN??? 1/1:0??? 1/1:0??? 1/1:0
> 12??? 121999716 <callto:12 121999716> CFAP251_Corrpad_exon20/22??? 
> .??? <DEL> .??? . 
> SVTYPE=DEL;END=121999944;CSQ=deletion|inframe_deletion&feature_truncation|MODERATE|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|20/22||||3132-3359|3008-3235|1003-1079|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|1/3||||2832-3059|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||1760|1||HGNC|HGNC:28506 
> GT:CN??? 1/1:0??? 1/1:0??? 1/1:0
> 12??? 122001497 <callto:12 122001497> CFAP251_Corrpad_exon21/22??? 
> .??? <DEL> .??? . 
> SVTYPE=DEL;END=122001598;CSQ=deletion|frameshift_variant&feature_truncation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|21/22||||3361-3461|3237-3337|1079-1113|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|2/3||||3061-3161|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||106|1||HGNC|HGNC:28506 
> GT:CN??? 1/1:0??? 1/1:0??? 1/1:0
>
>
>       System
>
>   * VEP version: 104.3
>   * VEP Cache version: homo_sapiens_vep_104_GRCh38
>   * Perl version: perl-5.16.3-299.el7_9.x86_64
>   * OS: centos 7
>   * tabix installed ? yes
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
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