[ensembl-dev] Variant effect predictor

[Will McLaren]

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?

>
> 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.

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
>
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