[ensembl-dev] Different chromosome names

[Kim Brugger]

The reference genomes (human, mouse, zebrafish) is maintained by the GRC 
(http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/) and not 1000 
genomes, though 1kg data is being used to assess reference errors. I no 
longer works in the GRC groups, so my knowledge might be slightly off, 
but others on this list should know the current status.

As you might have noticed two patches to the GRCh37 was recently 
released, representing a correction of part of the genome and a addition 
of novel sequence. As far as I know this is the way the reference 
genomes are going to be fixed/evolve for the foreseeable future. But I 
recall talk of an reference, containing all the known common variation. 
I.e. by including alternative assemblies and corrections. If you do any 
SNP calling you are probably aware of a heap of reference errors, there 
was talk about patching these, but depending on how it is done this 
might affect genome browsers.

The decision of the future of the reference genomes lies with the GRC 
SAB, and the people that does the work. So I am sure that they will 
appreciate any input that you give them through the webpage mentioned above.

/Kim


On 11/23/10 2:41 PM, Neil Walker wrote:
> Hi Gavin
>
>> I have noticed that Havana genes etc seem to annotate a different 
>> format of chromosome name e.g. HSCHR6_MHC_DBB.
>>
>>
>>
>> Simply out of curiosity can someone tell me why this occurs?
>
> By coincidence, we were looking at this yesterday:
>
> http://www.ensembl.org/Homo_sapiens/Info/Content?file=haplotypes.html
>
> Basically, some regions of the genome are so polymorphic *and*
> important, that a few alternative named haplotypes have been assembled.
>
> I'd actually quite like to know where this is going under the influence
> of the 1000 Genomes - is the *whole* genome going to get these
> alternative haplotypes, or is there some other cunning plan to represent
> relative and absolute positions?
>
> Cheers
> Neil
>


-- 
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Kim Brugger
EASIH, University of Cambridge
www.easih.ac.uk
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