[ensembl-dev] Allele specific custom annotation

Thu Mar 27 15:02:05 GMT 2014

Dear Will,

That would be great.

When do you think the next version will be released?

Thank you,

Adam

Adam P. Levine

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 27 March 2014 10:30
To: Ensembl developers list
Subject: Re: [ensembl-dev] Allele specific custom annotation

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<mailto: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> [mailto: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> [mailto: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<mailto: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<http://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<http://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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