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

Will McLaren wm2 at ebi.ac.uk
Thu Jul 7 09:53:40 BST 2016


Yes, you should make sure always that you match the assembly used to call
your variants with the assembly version in VEP.

Typically you will find this information in the header of the VCF generated
by your variant caller.

Will

On 7 July 2016 at 09:45, cy_jiang <cy_jiang at 126.com> wrote:

> Thank you very much for your quick response!
> Does it mean that other chromosome may exists the same problem if the
> reference we use is GRCh37 and VEP version 77?
>
> Thanks,
> Emma
>
>
>
>
>
> At 2016-07-07 16:36:33, "Will McLaren" <wm2 at ebi.ac.uk> wrote:
>
> Ensembl, and VEP, switched to GRCh38 by default from release 76 onwards.
>
> GRCh37 is still available as a database connection or cache download, but
> the default is to use GRCh38.
>
> Regards
>
> Will
>
> On 7 July 2016 at 09:13, cy_jiang <cy_jiang at 126.com> wrote:
>
>> Hi Will,
>> I am also interested in this problem.
>>
>> It seems that this is based on GRCh38.
>> $ 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
>>
>> I look into this position(chrM:4249) in UCSC Genome Browser on Human Feb.
>> 2009 (GRCh37/hg19) Assembly. It turns out that the base at this position is
>> T not C.
>> When changing it to GRCh38, it changes to C.
>>
>> As far as I am can remember, VEP version 77 is based on GRCh37. Did I
>> miss something there?
>>
>> Emma
>>
>>
>>
>>
>> At 2016-07-07 10:02:52, "林琼芬" <qiongfen0 at gmail.com> wrote:
>>
>> Dear Will,
>> Thank you so much. It do help me a lot, I have find out the bug and
>> trying to solve, thanks!
>>
>> Best Regard!
>> Lin
>>
>>
>> 2016-07-06 18:23 GMT+08:00 Will McLaren <wm2 at ebi.ac.uk>:
>>
>>> 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
>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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:
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>>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list    Dev at ensembl.org
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Arron Lin
>>>>
>>>> BGI Research Institute
>>>>
>>>> Email: qiongfen0 at gmail.com
>>>>
>>>> Beishan Industrial Zone| Yantian  District| Shenzhen 518083
>>>>
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>>>
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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:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
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