[ensembl-dev] Allele specific custom annotation

[Levine, Adam]

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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