[ensembl-dev] VEP annotation V2.2 and --most_severe

[Will McLaren]

Hi Salih,

You'd have a to write a small perl script to do this, as the
consequence rankings are stored internally in our API.

You will need to import the consequence type hash into your script as follows:

my %cons = %Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES;

# assuming you are using the Ensembl (default) consequence terms
# create a hash with the consequence name and rank
my %ranks = map {$_->{display_term} => $_->{rank}} %cons;

# now we can sort a list of consequences by their rank
my @cons_list = qw(NON_SYNONYMOUS_CODING FRAMESHIFT_CODING NMD_TRANSCRIPT);

# lowest rank number is most severe
my @sorted = sort {$ranks{$a} <=> $ranks{$b}} @cons_list;

Hope this helps,

Cheers

Will

On 23 May 2012 18:32, Fiona Cunningham <fiona at ebi.ac.uk> wrote:
>  Dear Salih,
>
> Apologies, I'm not sure if I followed exactly what you want to do
> here. Would this be equivalent to doing something like a 'diff' on the
> 2 different output files? Maybe this would solve your problem.
>
> Best wishes,
>
> Fiona
>
> -----------------------------------------------------------------------------------
> Fiona Cunningham
> Ensembl Coordinator, Ensembl Variation Project Leader.
> EMBL-EBI, Genome Campus, Hinxton, UK
> www.ensembl.org || www.lrg-sequence.org
> fiona at ebi.ac.uk   || t: +44 1223 494612
>
>
> On 20 May 2012 09:58, Salih Tuna <st5 at sanger.ac.uk> wrote:
>> Apologies,
>> I meant the option --per_gene for the most severe consequences...
>>
>>
>>
>> On 20/05/2012 09:27, "Salih Tuna" <st5 at sanger.ac.uk> wrote:
>>
>> Hi,
>> I am using VEP annotation V2.2
>> I did some annotation without using the option —most_severe. Now I would
>> like to eliminate the most severe ones for each gene. Is it possible to run
>> just this single module rather than running whole code again?
>>
>> Thanks,
>> Salih
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