[ensembl-dev] Variant effect predictor

Will McLaren wm2 at ebi.ac.uk
Wed Jun 15 14:34:05 BST 2011


Hello,

The next release of Ensembl is scheduled for the end of this month
(28th June) - the code will be ready then.

Cheers

Will

On 15 June 2011 13:18, Henrikki Almusa <henrikki.almusa at helsinki.fi> wrote:
> On 2011-06-15 15:32, Will McLaren wrote:
>>
>> Hi Henrikki,
>>
>> On 15 June 2011 12:05, Henrikki Almusa<henrikki.almusa at helsinki.fi>
>>  wrote:
>>>
>>> Hi,
>>>
>>> I'm testing the variant effect predictor (2.0 against local copy of
>>> ensembl
>>> 62) and noticed some things.
>>>
>>> 1. When I run one sample' indels with it, the resulting list has lines
>>> which
>>> start with '+' instead of the uploaded variation information. What causes
>>> this?
>>
>> I'm not sure what might be causing this - can you send me a sample
>> line of input that causes this problem?
>
> I managed to track this down and actually it was caused by an error in my
> own file transformation (I had comma instead of forward slash in allele). I
> had a situation where there was two variant alleles and my script didn't
> convert the comma between them. Sorry for the noise on this one.
>
>>>
>>> 2. It seems that the whole_genome option switches off the gene name. Is
>>> there an option to switch it back on? I could use HGNC to get that name,
>>> but
>>> would still lack the ensembl identifier.
>>
>> At the moment this option is missing - it will be added in the next
>> release of the script.
>
> Is there any plan when the update happen (so that I should go to download a
> new version)? There seems to be somewhat a difference in speed when putting
> exome sample though variant effect predictor between using the whole_genome
> and not.
>
>> The reason the gene name is switched off is that the script has to
>> query the database for every transcript to get the gene name, which
>> greatly slows down the process.
>>
>> It is also trivial to get the gene ID from the transcript ID - either
>> search for the ID on the Ensembl website, or query for it using the
>> API ($gene_adaptor->fetch_by_transcript_stable_id('ENST000000001') )
>>
>>>
>>> 3. The variant effect predictor seems to be able to read in the ucsc used
>>> 'chr1' type chromosomes. However it does stumble with 'chrM' which is
>>> 'MT'
>>> in ensembl.
>>
>> Thanks for spotting this - it's a bug, we should convert chrM to MT.
>>
>> Regards
>>
>> Will McLaren
>> Ensembl Variation
>>
>>>
>>> --
>>> Henrikki Almusa
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> List admin (including subscribe/unsubscribe):
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>
>
>
> --
> Henrikki Almusa
>




More information about the Dev mailing list