[ensembl-dev] Question regarding rs#'s - location only vs. location + nucleotide

[Jennifer Yen]

Hi Will,

Thanks - reinstalling the cache worked.

Best
Jenn



On Thu, Jun 25, 2015 at 7:54 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Jenn,
>
> Can you provide more details of this please?
>
> - Which VEP version are you using?
> - which cache (GRCh37 or GRCh38, RefSeq or Ensembl or merged)?
> - have you run convert_cache.pl?
>
> If possible are you able to provide a sample of input and a command line
> that reproduces this error?
>
> If the error occurs with the example_GRCh3*.vcf files provided alongside
> the script, I'd try re-installing VEP and the cache.
>
> Thanks
>
> Will McLaren
> Ensembl Variation
>
> On 24 June 2015 at 17:54, Jennifer Yen <jennifer.yen at personalis.com>
> wrote:
>
>> Hi Will,
>>
>> The --check_alleles flag generates an error when it starts checking for
>> existing variations. ("Use of uninitialized value in list assignment at
>> VEP.pm line 5130, <DUMP>".)  The vep script runs fine without the flag
>> though - anyone else have problems with this?
>>
>> Jenn
>>
>> On Wed, Jun 24, 2015 at 12:54 AM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>
>>> Hello Mollie,
>>>
>>> The VEP can compare the alleles of your input with those from the rs#
>>> variants; select "Yes and compare alleles" from the "Find co-located known
>>> variants:" dropdown menu under the "Identifiers and frequency data" tab
>>> when you submit your job.
>>>
>>> In the standalone tool, you must add the "--check_alleles" flag.
>>>
>>> Online:
>>> http://www.ensembl.org/info/docs/tools/vep/online/input.html#ident
>>> Standalone:
>>> http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_check_existing
>>>
>>> Regards
>>>
>>> Will McLaren
>>> Ensembl Variation
>>>
>>> On 23 June 2015 at 20:22, Ullman-Cullere, Mollie <
>>> MULLMANCULLERE at partners.org> wrote:
>>>
>>>> The rs# is a location identifier, where theoretically one rs# may have
>>>> multiple variants A/T, A/C, A/G.  To muddy the waters further, you may have
>>>> A/T somatic, A/T germline etc...
>>>>
>>>> I've been testing VEP GRCh 37 (online version) and found the rs# is
>>>> returned on a matching of location and not location + nucleotide change.
>>>> Would you please confirm functionality for both the online and
>>>> standalone tools?
>>>>
>>>> Best regards,
>>>> Mollie
>>>>
>>>> Mollie Ullman-Cullere
>>>> Sr. Clinical Bioinformaticist
>>>> Clinical and Translational Informatics
>>>> Dana-Farber Cancer Institute/Partners Healthcare
>>>>
>>>>
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom
>>>> it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>> e-mail
>>>> contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>>> in error
>>>> but does not contain patient information, please contact the sender and
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>>>
>>>> _______________________________________________
>>>> Dev mailing list    Dev at ensembl.org
>>>> Posting guidelines and subscribe/unsubscribe info:
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>
>> ------------------------------
>> This email and any files transmitted with it are confidential and
>> intended solely for the use of the individual or entity to whom they are
>> addressed. This message may contain privileged and / or confidential
>>  information. If you are NOT the intended recipient of this message,
>> copying, printing, disseminating, forwarding or any other use or action
>> derived from its content is strictly prohibited. Please notify the sender
>> immediately by e-mail if you have received this e-mail by error and delete
>> this e-mail from your system. If you received the email by error and this
>> message contains patient information, please report the error by contacting
>> the Personalis Clinical Laboratory at clinical at personalis.com.
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>

-- 

------------------------------
This email and any files transmitted with it are confidential and intended 
solely for the use of the individual or entity to whom they are addressed. 
This message may contain privileged and / or confidential  information. If 
you are NOT the intended recipient of this message, copying, printing, 
disseminating, forwarding or any other use or action derived from its 
content is strictly prohibited. Please notify the sender immediately by 
e-mail if you have received this e-mail by error and delete this e-mail 
from your system. If you received the email by error and this message 
contains patient information, please report the error by contacting the 
Personalis Clinical Laboratory at clinical at personalis.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150629/a4b4fc58/attachment.html>