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

[Jennifer Yen]

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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150624/ca04594a/attachment.html>