[ensembl-dev] Allele specific custom annotation
Will McLaren
wm2 at ebi.ac.uk
Mon Mar 10 15:43:28 GMT 2014
Hi Adam,
Currently there is no way to do allele-specific annotation with the
--custom flag alone.
If you are not averse to a bit of coding you could write a plugin to do
that for you; you could either write the plugin to fetch the scores for you
(the VEP is simply piping in tabix output), or have the plugin post-process
the scores added as you have them above (this would require writing the
least code).
http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
Our dbNSFP plugin does something similar:
https://github.com/ensembl-variation/VEP_plugins/blob/master/dbNSFP.pm
Regards
Will McLaren
Ensembl Variation
On 10 March 2014 15:30, Levine, Adam <a.levine at ucl.ac.uk> wrote:
> I have a query regarding performing custom annotation using the VEP. I
> would like to annotate specific allele changes with a score, i.e. a G to T
> with score X but G to A at the same position with score Y. It seems,
> however, that the VEP only annotates on the basis of position and does not
> consider the allele change. Am I correct? If so, is there a way to set it
> to use custom annotation tracks in an allele specific manner?
>
>
>
> The custom annotations are in VCF format, e.g.:
>
>
>
> ##fileformat=VCFv4.0
>
> #CHROM POS ID REF ALT QUAL FILTER
> INFO
>
> 21 26960070 GT_scoreX G T .
> . .
>
> 21 26960070 GA_scoreY G A .
> . .
>
>
>
> The input file looks like this:
>
>
>
> ##fileformat=VCFv4.0
>
> #CHROM POS ID REF ALT QUAL FILTER
> INFO
>
> 21 26960070 rs116645811 G A .
> . .
>
>
>
> My command is:
>
>
>
> perl variant_effect_predictor.pl \
>
> --input_file example_single_variant.vcf \
>
> --format vcf \
>
> --custom test_custom.vcf.gz,test_custom,vcf,exact \
>
> --cache
>
>
>
> The output looks like this:
>
>
>
> ## ENSEMBL VARIANT EFFECT PREDICTOR v75
>
> ## Output produced at 2014-03-10 14:34:53
>
> ## Connected to homo_sapiens_core_75_37 on ensembldb.ensembl.org
>
> ## Using cache in /home/Levine/.vep/homo_sapiens/75
>
> ## Using API version 75, DB version 75
>
> ## Extra column keys:
>
> ## DISTANCE : Shortest distance from variant to transcript
>
> ## STRAND : Strand of the feature (1/-1)
>
> ## test_custom : test_custom.vcf.gz (exact)
>
> #Uploaded_variation Location Allele Gene Feature
> Feature_type Consequence cDNA_position CDS_position
> Protein_position Amino_ac
>
> ids Codons Existing_variation Extra
>
> rs116645811 21:26960070 A ENSG00000260583
> ENST00000567517 Transcript upstream_gene_variant
> - - - - - -
>
> STRAND=-1;test_custom=GT_scoreX,GA_scoreY;DISTANCE=4432
>
> rs116645811 21:26960070 A ENSG00000154719
> ENST00000352957 Transcript intron_variant -
> - - - - - STRAND=-
>
> 1;test_custom=G_A,G_T
>
> rs116645811 21:26960070 A ENSG00000154719
> ENST00000307301 Transcript missense_variant 1043
> 1001 334 T/M aCg/aTg -
>
> STRAND=-1;test_custom=GT_scoreX,GA_scoreY
>
>
>
> You can see the variant in the input (G>A) is annotated with both G_A and
> G_T. I can of course, pull out the relevant annotation (score X for G>T,
> score Y for G>A) myself manually after the fact but it would be great if
> the VEP could do it directly.
>
>
>
> Thank you,
>
>
>
> Adam
>
>
>
> Adam P. Levine
>
>
>
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