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

Thu Jul 7 09:13:02 BST 2016

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
Date: 2016-06-28 17:30
To: Ensembl developers list
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

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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

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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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Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
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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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