[ensembl-dev] different between eGenetics and GNF/Atlas

Wed Jul 6 11:23:50 BST 2016

The reference allele is incorrect in your input. If you specify
--check_ref, VEP will warn you that the allele is wrong (and tell you what
the correct allele is) and ignore that input:

$ echo "MT 4249 . T C" | perl variant_effect_predictor.pl --database
--force --check_ref
2016-07-06 11:18:22 - Reading input from STDIN (or maybe you forgot to
specify an input file?)...
2016-07-06 11:18:22 - Starting...
2016-07-06 11:18:22 - Detected format of input file as vcf

WARNING: Specified reference allele T does not match Ensembl reference
allele C on line 1
2016-07-06 11:18:22 - Wrote stats summary to
variant_effect_output.txt_summary.html
2016-07-06 11:18:22 - See variant_effect_output.txt_warnings.txt for
details of 1 warnings
2016-07-06 11:18:22 - Finished!

Here's the HGVS output with the correct input (assuming that the ref/alts
are switched):

$ echo "MT 4249 . C T" | perl variant_effect_predictor.pl -data -force
-pick -check_ref -fields HGVSc,HGVSp -o stdout -hgvs | grep -v #
ENST00000361390.2:c.943C>T      ENSP00000354687.2:p.Pro315Ser

Regards

Will

On 6 July 2016 at 10:38, 林琼芬 <qiongfen0 at gmail.com> wrote:

> Hello Will,
> Thanks for you help. I have try the two method you give, but it doesn't
> work. Reference allele has no problem, so as "MT". If there have any other
> solution？
>
> Best regard!
> Lin
>
> 2016-07-04 16:25 GMT+08:00 Will McLaren <wm2 at ebi.ac.uk>:
>
>> Hello Lin,
>>
>> There is a problem with your input - the reference allele that you have
>> specified does not match the reference genome sequence. You can have VEP
>> check your input for this issue by adding --check_ref to your command line.
>>
>> You should also use "MT" to refer to the mitochondrial chromosome in
>> place of "M".
>>
>> Regards
>>
>> Will McLaren
>> Ensembl Variation
>>
>> On 4 July 2016 at 03:53, qiongfen0 at gmail.com <qiongfen0 at gmail.com> wrote:
>>
>>> Dear Thomas,
>>> Thanks for your reply, it has help me so much.
>>> Now, I have another confused, I hope you can help me understand this.
>>> I am using ensembl-tools-release-77 now, when I use VEP to annotate the
>>> variants in mitochondria, some has the result of HGVSp but not have HGVSc
>>> (like the follow printscreen), it may be quiet strange. Then I use the
>>> VEP online  to try again, but it has no result of HGVSc and HGVSp. I
>>> wonder what make this result appear.
>>>
>>>
>>> Hope to hear form you.
>>>
>>> Yours sincerely,
>>> Lin
>>>
>>> *From:* Thomas Maurel <maurel at ebi.ac.uk>
>>> *Date:* 2016-06-28 17:30
>>> *To:* Ensembl developers list <dev at ensembl.org>
>>> *Subject:* Re: [ensembl-dev] different between eGenetics and GNF/Atlas
>>> Dear Lin,
>>>
>>> I am afraid that this data was retired in Ensembl release 76. These
>>> might not match as the data is coming from two different sources:
>>>
>>> GNF/Atlas data came to us via the Gene Expression Atlas project at
>>> EMBL-EBI.
>>>
>>> http://www.ebi.ac.uk/gxa/
>>>
>>> The GNF/Atlas data was published by the Genomics Institute of the
>>> Novartis Research Foundation:
>>>
>>> http://www.gnf.org/technology/organismal/gene-expression-core.htm
>>>
>>> The eGenetics database uses Expressed Sequence Tags (ESTs) annotated
>>> with eVOC ontology terms by SANBI (South African National Bioinformatics
>>> Institute). More information below.
>>>
>>> http://www.ncbi.nlm.nih.gov/pubmed/12799354
>>> http://www.sanbi.ac.za/
>>>
>>> Hope this helps,
>>> Best Regards,
>>> Thomas
>>>
>>> On 28 Jun 2016, at 03:04, qiongfen0 at gmail.com wrote:
>>>
>>> Dear Sirs,
>>> I'm using biomart to filter a series of genes which are specifically
>>> expressed in the brain. In biomart there are two such filters,
>>> 'eGenetics/SANBI EST anatomical system data' and 'GNF/Atlas organism part',
>>> however, the results of these two filters don't match. I searched for it at
>>> biomart help but i couldn't find anything about this. Can anybody help me
>>> to understand the difference of these two filters?
>>> I am looking forward to hearing from you.
>>>
>>> Yours sincerely,
>>> Lin
>>>
>>> Qiongfen Lin
>>> South China Normal University
>>> TEL: +8615118845463| Mail : qiongfen0 at gmail.com
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
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>>>
>>>
>>> --
>>> Thomas Maurel
>>> Bioinformatician - Ensembl Production Team
>>> European Bioinformatics Institute (EMBL-EBI)
>>> European Molecular Biology Laboratory
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom
>>>
>>>
>>> _______________________________________________
>>> 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:
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>>
>>
>
>
> --
>
> Arron Lin
>
> BGI Research Institute
>
> Email: qiongfen0 at gmail.com
>
> Beishan Industrial Zone| Yantian  District| Shenzhen 518083
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
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