[ensembl-dev] "subseq" error
S Venkata Suresh Kumar
suresh.surampudi at india.semanticbits.com
Wed Feb 29 08:06:04 GMT 2012
I am using a file (without header) with one HGVS syntax :
I am trying to convert this into VCF (to test vep script). Following is
the way I am trying:
$ perl /opt/vep/variant_effect_predictor.pl -i hgvs -o hgvs.vcf -refseq
-convert vcf --verbose -force
On 02/28/2012 10:55 PM, Will McLaren wrote:
> Are you able to provide an example of the line that is causing this issue?
> Will McLaren
> Ensembl Variation
> On 28 February 2012 11:13, S Venkata Suresh Kumar
> <suresh.surampudi at india.semanticbits.com> wrote:
>> Hi All
>> When i am trying to convert a hgvs file to vcf file, I am getting
>> following error:
>> "Can't call method "subseq" on an undefined value at
>> line 1272, <GEN0> line 1."
>> any clues ?
>> I am using vep 2.4, OS linux, bioperl 1.6.901-2.
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