[ensembl-dev] Allele specific custom annotation

Will McLaren wm2 at ebi.ac.uk
Thu Mar 27 10:30:16 GMT 2014


Hi Adam,

It's something we're looking at for the next version of the VEP.

Regards

Will


On 26 March 2014 17:09, Levine, Adam <a.levine at ucl.ac.uk> wrote:

>  I previously enquired about allele specific custom annotation. On a
> related theme, would it be possible for the VEP to be configured to report
> the allele frequency (from 1KG and ESP) of the actual alternate allele as
> opposed to just the MAF at that position? Obviously, this is important for
> multiallelic variants and filtering on MAF may result in the exclusion of a
> rare variant of interest due to the occurrence of a common variant at the
> same position.
>
>
>
> Thank you,
>
>
>
> Adam
>
>
>
> Adam P. Levine
>
>
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Levine, Adam
> *Sent:* 10 March 2014 15:53
>
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] Allele specific custom annotation
>
>
>
> Dear Will,
>
>
>
> Thank you for your prompt reply.
>
>
>
> Sure, I will write a script to do it.
>
>
>
> Kind regards,
>
>
>
> Adam
>
>
>
> Adam P. Levine
>
>
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Will McLaren
> *Sent:* 10 March 2014 15:43
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] Allele specific custom annotation
>
>
>
> 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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