[ensembl-dev] allele-specific annotation against a custom VCF

Will McLaren wm2 at ebi.ac.uk
Tue May 19 10:28:25 BST 2015

Hi Katherine,

As you've observed, currently the custom annotation feature does not take
the allele from the VCF into account when reporting annotations.

If you are particularly interested in adding the ExAC data, we have
available an ExAC plugin that does this while taking into account the



Will McLaren
Ensembl Variation

On 14 May 2015 at 20:45, Katherine Smith <
katherine.smith at genomicsengland.co.uk> wrote:

> Dear ENSEMBL developers,
> Is there any way to make VEP custom annotation against a VCF file
> allele-specific?
> The custom annotation help page says "Users should note that the VEP will
> only look for overlaps (both exact and inexact) with these annotations; for
> example, any sequence in a GTF file will not be taken into account." (
> http://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html)
> I am using VEP 79 to annotate a VCF against allele counts from two VCF
> files using --custom. One VCF file is the ExAC r0.3 file (
> ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ExAC.r0.3.sites.vep.vcf.gz);
> this can contain multiple alternate alleles separated by a comma, e.g.
> 1       20395401        rs11573185      C       A,G,T   6372227.62
> PASS    AC=7149,3,1
> The second VCF file is 'normalised' so that a variant location with two
> alternate alleles is represented as two separate lines, each with only one
> alternate allele.
> 1       20395401        .       C       A       709     .       AC=2154
> 1       20395401        .       C       G       95      .       AC=1
> I have a sample with a heterozygous C/A genotype. The INFO tag added for
> ExAC is "ExAC.r0.3_AC=7149,3,1", i.e. it adds the allele count for all
> alternate alleles, although only one is observed in this sample. The tag
> AC=1 is added for the other database, i.e. it adds the allele count for the
> G allele, which is not observed, rather than the A allele, which is.
> Is there a way to make VEP only report the annotations for the alternate
> allele(s) observed in the input VCF?
> I am running variant_effect_predictor.pl with options `--check_existing`
> and `--check_alleles` and custom annotation is performed using e.g.
> `--custom ExAC.r0.3.sites.vep.vcf.gz,ExAC.r0.3,vcf,exact,0,AF,AC,AN`
> Many thanks for your advice,
> Katherine
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