[ensembl-dev] Variant Effect Predictor

[Will McLaren]

(Forgot to copy in to the list first time!!!)

To get the rsIDs, you would need to add the following line to the config file:

check_existing    1

as this is not enabled by default in the standalone script.

The code that reads config files expects you to have a value after
each flag, so to enable e.g. HGNC the line should be:

hgnc    1

Apologies for this, as the documentation here is not clear.

Thanks

Will McLaren
Ensembl Variation

On 23 January 2012 15:03, Aparna Radhakrishnan <ar10 at sanger.ac.uk> wrote:
> Hi. I ran the VEP web version using the first 750 SNPs in my large file. I
> had ticked on the following options:
>
> 1) Input file format : Ensembl default
> 2) Check for existing co-located variant : Yes and compare alleles
> 3) Show HGNC identifier for gene where available
> 4) SIFT predictions : Prediction and score
> 5) PolyPhen predictions : Prediction and score
> 6) Condel consensus (SIFT/PolyPhen) predictions : Prediction and score
>
> This returned all the expected columns and values.
>
> However, on downloading and running the stand-alone perl script using a
> config file which is as below:
>
> terms ensembl
> sift b
> polyphen b
> condel b
> regulatory
> gene
> hgnc
> ccds
>
> check_ref
> check_alleles
> output_file myout
> species	homo_sapiens
> format ensembl
> input_file VEP_1.inp
>
>
> The script does not return the HGNC or the rsID for co-located variants.
>
> Any help on why this might be the case would be of great help.
>
> Regards,
> Aparna.
>
> Hi. I ran the VEP web version using the first 750 SNPs in my large file. I
> had ticked on the following options:
>
> 1) Input file format : Ensembl default
> 2) Check for existing co-located variant : Yes and compare alleles
> 3) Show HGNC identifier for gene where available
> 4) SIFT predictions : Prediction and score
> 5) PolyPhen predictions : Prediction and score
> 6) Condel consensus (SIFT/PolyPhen) predictions : Prediction and score
>
> This returned all the expected columns and values.
>
> However, on downloading and running the stand-alone perl script using a
> config file which is as below:
>
> terms ensembl
> sift b
> polyphen b
> condel b
> regulatory
> gene
> hgnc
> ccds
>
> check_ref
> check_alleles
> output_file myout
> species homo_sapiens
> format ensembl
> input_file VEP_1.inp
>
>
> The script does not return the HGNC or the rsID for co-located variants.
>
> Any help on why this might be the case would be of great help.
>
> Regards,
> Aparna.
>
>
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