[ensembl-dev] Possible bug in VEP(v73)

[Fiona Cunningham]

Dear Saurabh,

Many thanks for taking the time to report this to us. We will take a look.

Best regards,
Fiona

---------------------------------------------------------------------------------------------------------------
Fiona Cunningham, Ensembl Coordinator, Ensembl Variation Project Leader.
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton,  CB10 1SD, UK
www.ensembl.org || www.lrg-sequence.org || t: +44 1223 494612


On 18 October 2013 07:22, saurabh gupta <saurabh at ganitlabs.in> wrote:
> Hi,
>
> I had downloaded the standalone version of VEP(v73) and was using it
> offline. When I tried using --hgvs with --offline I was getting an error:
> "ERROR: Cannot generate HGVS coordinates in offline mode without a FASTA
> file (see --fasta)". However I had specified the --fasta option as well.
> After going through the code it seems the condition(line 954) is checking if
> $config{fasta_db} is defined or not and throwing this error. In the code
> $config{fasta_db} is initialized at a later stage, so it throws an error.
>
> I changed $config{fasta_db} to $config{fasta} on line 954(where the
> condition is checked) in variant_effect_predictor.pl and it worked.
>
> You guys might want to incorporate/modify this in the code.
>
> --
> Saurabh Gupta
> Ganit Labs, Bangalore
>
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