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

saurabh gupta saurabh at ganitlabs.in
Fri Oct 18 07:22:53 BST 2013


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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