[ensembl-dev] Variant Effect Predictor

[Aparna Radhakrishnan]

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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