[DAS] Survey on DAS projects

Fri Nov 18 15:24:59 UTC 2011

Hi Andy,

thanks for the info. Having a bed DAS adaptor is part of the problem,
the other is not having to worry about having to deal with the DAS
server directly. easyDAS manages to do this but unfortunately it is
not obvious for people who do not know DAS how to operate it. Also if
the file is very big and the connection slow it can take up to an hour
to create a DAS source.

Wouldn't it be nice to create a DAS source just with one click or two?

Please see below a snippet of a few SNPs in my chromosome 16 just as
you would get them from 23andMe (NCBI36 assembly; columns mean
SNP_id/chr/position/genotype).

Cheers,
Manuel

rs7763	16	544555	TT
rs763158	16	546105	GG
rs7190878	16	549131	AG
rs4984890	16	552699	CT
rs710925	16	573355	AG
rs2017567	16	577213	CT
rs4144003	16	585969	CT
rs7190358	16	590789	AG
rs7203694	16	592942	AG
rs11248940	16	595687	TT
rs7204088	16	601143	TT
rs4984677	16	611683	AG
rs9929621	16	619413	CT
rs11642546	16	641657	CC
rs3752496	16	650256	TT
rs2301426	16	651906	GG
rs1044662	16	655061	CC
rs9934288	16	656288	AC
rs3752493	16	657524	TT
rs1139897	16	660987	GG
rs1045763	16	664085	CC
rs3830140	16	665336	AA
rs8056588	16	666190	CC
rs6597	16	671726	TT

Manuel Corpas, PhD
Tel:      +44.122349.2372
Web:    http://manuelcorpas.com/about/
Twitter: @manuelcorpas

On 18 November 2011 15:14, Andy Jenkinson <andy.jenkinson at ebi.ac.uk> wrote:
> Hi Manuel,
>
> Since 2008 ProServer has had a BED format SourceAdaptor (called bed12, as it is intended to work with the 12-field BED format). It also supports Hydras, which are modules that are designed to automatically create DAS sources from a single config without restarting the server. This is how EasyDAS works with ProServer: there is one SourceAdaptor, and a Hydra to scan a relational database for new data.
>
> I don't know what 23andme's data looks like, but the addition of a Hydra to scan directories for new files and automatically make them available as DAS sources would seem to be a trivial piece of work. I daresay a VCF adaptor would also be fairly easy, especially if there is a Perl API of some sort (BioPerl?).
>
> Cheers,
> Andy
>
> 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
>>
>> 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:
>>> Hi
>>>
>>> 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 it.
>>> 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 people
>>> 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 interested
>>> 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 Road,
>>> London, NW1 2BE._______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>>>
>>
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>
>