[Bioperl-l] Classifying SNPs

[Abhishek Pratap]

Hi Pablo
Many thanks for for your reply. I am currently attending a workshop so might
not get time to check out your suggestions. Once I am back I will get back
to you in case I have any questions.

Thanks,
-Abhi

On Tue, Jul 14, 2009 at 7:57 PM, Pablo Marin-Garcia <pg4 at sanger.ac.uk>wrote:

>
> fixing a typo and explaining a gotcha
>
> On Tue, 14 Jul 2009, Pablo Marin-Garcia wrote:
>
>
>> Hello Abhishek
>>
>> Ensembl has a module for calculate SNP consequences in a transcript.
>>
>> The script that they use to create their consequences is located in:
>>
>>
>> ensembl-55/ensembl-variation/scripts/import/parallel_transcript_variation.pl
>>
>> The important bit is to  convert your snp coordenates and the
>> variation_allele into a ConsequenceType object
>>
>> $consequence_type =
>> Bio::EnsEMBL::Variation::ConsequenceType->new($tr->dbID,$chr,$start,$end,$strand,\@alleles);
>>
>>
> fixing typo: (instead $chr it would be a $variation_id)
>
>
> Bio::EnsEMBL::Variation::ConsequenceType->new($tr->dbID,$var_id,$var_start,$var_end,$var_strand,\@alleles);
>
> warning:
>
> The transcript_id and the variation_id are not important if you are not
> building a ensembl database.
>
> BUT the gotcha part is that the start and end of the variation should refer
> to the same slice start than the transcript used in the next step
> (type_variation). Be careful because depending how you select the gene or
> slice to retrieve your transcripts your transcript start and end would be
> the chromosome coordinates or a relative start/end from the slice start.
>
> You should work with chr positions for the variations and the transcripts
> (where start/end == seq_region_start/seq_region_end) to avoid problems.
>
>  and pass this and a transcript to the  type_variation
>> Bio::EnsEMBL::Utils::TranscriptAlleles exported method
>>
>>  $consequences = type_variation($tr, $gene, $consequence_type);
>>
>>
> The $gene is optional
>
>
>  in the module
>>
>> ensembl-55/ensembl/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm
>>
>> The other important bit in this script is that now the functional_genomics
>> consequences are calculated in this script instead in the type_variation()
>>
>> The only drawback is that it return only the ensembl classes of
>> consequences , but you can extend that later if you need more specific
>> consequences (I have done that in the past for different projects).
>>
>> This ensembl aproach will save you a lot of problems with the mapping from
>> gene to protein and with multiple snps in a codon.
>>
>> If you have experience with ensembl then is easy to follow the code. If
>> not you can always ask for help in the ensembl-dev mailing list (
>> ensembl-dev at ebi.ac.uk)
>>
>>
>> If you want to read the code without checking out the whole api:
>>
>>
>>
>> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/scripts/import/parallel_transcript_variation.pl?revision=1.27&root=ensembl&view=markup
>>
>> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Utils/TranscriptAlleles.pm?root=ensembl&view=log
>>
>>
>> hope this helps
>>
>>
>>  - Pablo
>>
>>
>>
>>
>>
> =====================================================================
>                     Pablo Marin-Garcia, PhD
>
>                    \\//          (Argiope bruennichi
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>
> Sanger Institute                |  PostDoc / Computer Biologist
> Wellcome Trust Genome Campus    |  team : 128/108 (Human Genetics)
> Hinxton, Cambridge CB10 1HH     |  room : N333
> United Kingdom                  |  email: pablo.marin at sanger.ac.uk
> ====================================================================
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