[ensembl-dev] Ensembl release 82 is out!

[Ivan Adzhubey]

Hi,

$ variant_effect_predictor.pl --offline --cache --assembly GRCh37 --format vcf -i 
example_GRCh37.vcf --everything -o example_annotated_GRCh37.vcf

2015-09-30 17:39:59 - Read existing cache info
2015-09-30 17:39:59 - INFO: Disabling --hgvs; using --offline and no FASTA file 
found
2015-09-30 17:39:59 - Starting...
2015-09-30 17:39:59 - Read 173 variants into buffer
2015-09-30 17:39:59 - Checking for existing variations
<...>
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
[============================>                                                                                                  
]   [ 23% ]Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
Use of uninitialized value in concatenation (.) or string at 
/net/apps/noarch/vep/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2757.
<...>

On Wednesday, September 30, 2015 01:41:00 PM Thomas Maurel wrote:
> We are pleased to announce that the latest Ensembl update (e!82) has been
> released: http://www.ensembl.org/ <http://www.ensembl.org/>
> 
> Highlights of this release include:
> 
> Ensembl mobile website <http://m.ensembl.org/>
> Support of VEP Plugins through the web interface, script and REST
> Improved Variation tables
> <http://e82.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?g=ENSG000001
> 39618;r=13:32315474-32400266> RNASeq data set of Zebrafish
> <http://e82.ensembl.org/Danio_rerio/Info/Index> developmental stages
> Marking a region on images
> LastZ replaced TBlat for pairwise alignments
> Human variation data updates to dbSNP (144) including variants from the
> Exome Aggregation Consortium (ExAC <http://exac.broadinstitute.org/>) Mouse
> <http://e82.ensembl.org/Mus_musculus/Info/Index>: updated to GENCODE M7
> including HAVANA annotation. Improved data upload form
> Improvements to PDF export
> Export mode for projectors and print
> Phenotype data updated for several species, including human
> <http://e82.ensembl.org/Homo_sapiens/Phenotype/Locations?ph=5815>, mouse
> <http://e82.ensembl.org/Mus_musculus/Phenotype/Locations?ph=225>, rat
> <http://e82.ensembl.org/Rattus_norvegicus/Phenotype/Locations?ph=73> and
> horse <http://e82.ensembl.org/Equus_caballus/Info/Index>
> 
> A complete list of the changes in release 82 can be found at
> http://www.ensembl.org/info/website/news.html
> <http://www.ensembl.org/info/website/news.html>
> 
> For the latest news from the Ensembl project visit our blog at
> http://www.ensembl.info <http://www.ensembl.info/>
> 
> The release 82 blog post can be viewed here:
> http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/
> <http://www.ensembl.info/blog/2015/09/30/ensembl-82-has-been-released/>
> 
> The e82 webinar is planned for Wednesday 7th Oct at 16:00 GMT+1, please
> register using the following URL (registration is free):
> http://www.ebi.ac.uk/training/events/2015/ensembl-release-82-webinar
> <https://attendee.gototraining.com/r/1571390501370151169>
> 
> 
> Best Regards,
> Thomas


-- 
Ivan Adzhubey, Ph.D.
Instructor
Division of Genetics, Dept of Medicine
Brigham & Women's Hospital
Harvard Medical School
New Research Building, Room 0464C
77 Avenue Louis Pasteur
Boston, MA 02115
tel.: (617) 525-4728
fax:  (617) 525-4705
web: http://genetics.bwh.harvard.edu/wiki/sunyaevlab/