[ensembl-dev] different between eGenetics and GNF/Atlas
Will McLaren
wm2 at ebi.ac.uk
Thu Jul 7 09:36:33 BST 2016
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:
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>>>>> 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/
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
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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
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>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> 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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