[ensembl-dev] Making annotations for data from hg18 or build36

[Laura Clarke]

The 1000 genomes project does have a ensembl 60 schema version (data
is still version 54) database available on NCBI 36

http://www.1000genomes.org/node/517

There is a version of the VEP though not the most modern one which
will work with this data

thanks

Laura

On Wed, Nov 30, 2011 at 2:52 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
> Hi Salih,
>
> What kind of annotations are you looking to do?
>
> You have two options:
>
> 1) Use the last Ensembl build to use NCBI36, which was e!54 (you will
> need the API from e!54). If you are looking to use the VEP, currently
> this isn't straightforward, but I have an experimental cache file
> built from NCBI36 coordinates that I could make available to you if
> this is your intention and you are willing to be a guinea pig!
>
> 2) Convert the coordinates you have to GRCh37 using Ensembl's assembly
> mapper tool:
>
> http://www.ensembl.org/tools.html
>
> Hope this helps!
>
> Will McLaren
> Ensembl Variation
>
> On 30 November 2011 11:12, Salih Tuna <st5 at sanger.ac.uk> wrote:
>> Hi,
>> I would like to make annotations for data whose reference is hg18.
>> I looked at the help file but couldn’t see the which parameters I should
>> change for hg18 or build36?
>>
>> Thanks for your help,
>> Salih
>>
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>
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