[DAS] Genotype MyDAS adapter
jw12 at sanger.ac.uk
Fri Nov 18 10:15:18 UTC 2011
Thanks Manuel, that's exactly the sort of reply we are hoping for.
It's great if people want to publicise what they are doing on the list.
In addition I should add that if people wish to distribute 23AndMe
data via DAS I have developed a very simple MyDAS adapter for this
purpose that comes with the current myDAS download (http://code.google.com/p/mydas/
Comprehensive instructions for setting up the database and uploading
the data file can be found here: http://biodasman.wordpress.com/2011/11/04/how-to-create-a-genotype-database-for-use-as-a-das-source/
The configuration for connecting to this database is also in MyDAS and
Obviously this isn't an automatic set-up via a pretty interface, but
it's relatively simple for anyone with a degree of technical ability
to do in the mean time.
On 17 Nov 2011, at 17:11, Manuel Corpas wrote:
> Dear Jonathan,
> I hope you do not mind me copying the DAS list in this email, as we
> would be very keen to gather interest in the community regarding DAS
> applications to whole genomes.
> We are interested in exploring DAS in the context of genomic variants
> (SNPs, indels, CNVs) from personal genomes plus their integration with
> relevant sources (genes, variation data, phenotypes).
> Currently we have done a lot of work with 23andMe (whole-genome)
> genotypes but now we are expecting to extend our efforts further to
> exome data. A critical tool we are currently missing is one that
> allows automatic creation of DAS sources via an API directly from bed
> format (used by 23andMe) or vcf (1000genomes).
> Anyone interested in discussing these topics please let me know.
> Kind regards,
> Manuel Corpas, PhD
> Tel: +44.122349.2372
> Web: http://manuelcorpas.com/about/
> Twitter: @manuelcorpas
> On 17 November 2011 12:11, Jonathan Warren <jw12 at sanger.ac.uk> wrote:
>> As the 2012 DAS workshop is coming up at the end of February we
>> would like
>> to hear from people using DAS.
>> We would be really grateful to receive just a short email from
>> anyone using
>> DAS or developing DAS with a brief summary about their project and
>> how DAS
>> fits in, especially if you have not spoken at the DAS workshops at
>> any time.
>> Please also say if you would be interested in giving a short
>> presentation at
>> the workshop in February even if you are not sure if you could make
>> Previous years the presentations have been 15 minutes with 5
>> minutes for
>> questions - however this year we intend to be more flexible and so
>> if you
>> would prefer to give a "lightning talk" of just 5 minutes to update
>> or give them a brief overview that will be fine. Links to the
>> previous years
>> talks can be found here http://www.biodas.org/wiki/DASWorkshop2011#Day_2
>> I must emphasise - please give us a summary even if you are not
>> in giving a talk as we would like to know what is going on out
>> there and we
>> promise not to hound you to give a talk :)
>> Thanks in advance
>> The Sanger/EBI DAS people.
>> Jonathan Warren
>> Senior Developer and DAS coordinator
>> blog: http://biodasman.wordpress.com/
>> jw12 at sanger.ac.uk
>> Ext: 2314
>> Telephone: 01223 492314
>> The Wellcome Trust Sanger Institute is operated by Genome
>> ResearchLimited, a
>> charity registered in England with number 1021457 and acompany
>> registered in
>> England with number 2742969, whose registeredoffice is 215 Euston
>> London, NW1 2BE._______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk
Telephone: 01223 492314
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
More information about the DAS