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

[Will McLaren]

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
>>>
>>>
>>>
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