[ensembl-dev] Variant Consequence Predictor

[Stuart Meacham]

Hi,

I wasn't using the 1000 Genomes browser but running the Variant effect 
predictor over the raw vcf data available from (25GB File be warned!!):

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/supporting/EUR.BI_withr2.20100804.genotypes.vcf.gz

Not sure how assemblies would effect the output . . .

Cheers

Stuart



On 25/02/11 09:45, Laura Clarke wrote:
> Hi Stuart
>
> the main ensembl browser and the 1000 genomes browser are using
> different assemblies , GRCh37 for ensembl and NCBI36 for 1000 genomes.
> The 1000 genomes browser is also using a older annotation set (ensembl
> 54) than main ensembl.
>
> These would be the first things I would check when trying to look for
> errors, is the cdna for this transcript the same between the 2
> browsers
>
> thanks
>
> Laura
>
> On Fri, Feb 25, 2011 at 9:23 AM, Stuart Meacham<sm766 at cam.ac.uk>  wrote:
>> Hi list (Will!),
>>
>> I have been using the Variant Consequence predictor in whole genome mode and
>> have (at least one) anomalous results. For example:
>>
>> Transcript: ENST00000260061
>>
>> SNP Residue Major Minor AA_Replacement Consequence
>>
>> rs79525962 407 C T A/P NON_SYNONYMOUS_CODING
>> 11_76371418_C/T 407 C T A/T NON_SYNONYMOUS_CODING
>>
>> top line is data in Ensembl
>> second line is data (1000 Genomes) using the predictor. You can see the
>> Consequence predictor shows an amino acid change (A/T) at the same position
>> as Ensembl shows A/P.
>>
>> Is one just wrong? And if so how do I check which one?
>>
>> Cheers
>>
>> Stuart
>>
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