[ensembl-dev] VEP cannot annotate * alternate alleles

[Will McLaren]

Hi Jessica,

The * allele is not annotated because there is nothing to annotate; it
represents the absence of any allele due to an upstream deletion. The
upstream deletion will of course be annotated.

Example:

REF:  ACGGTAGC
S1 :  ACG----C
S2 :  ACGGCAGC

There are two mutations here; one deletion in S1, and one SNP in S2.
Because the sequence containing the SNP is absent in S1, the genotype calls
for this site in individuals with the deletion are otherwise impossible to
annotate, unless you use the * notation.

So the VCF looks like this:

chr1 3 GGTAG G   ... 1/1 0/0
chr1 5 T     C,* ... 2,2 1/1

VEP will annotate the deletion as normal, but will only annotate the C ALT
allele for the SNP; the * represents the absence of an allele, so no
annotation is added - the deleted sequence is annotated for the variant on
the previous line.

Hopefully that makes sense!

If you can provide an example of where you think VEP is doing something
wrong then of course please do let us know.

Regards

Will McLaren
Ensembl Variation

On 13 November 2015 at 21:35, JESSICA X. CHONG <jxchong at uw.edu> wrote:

>
> http://gatkforums.broadinstitute.org/discussion/6240/what-means-is-in-alternative-allele
>
> Apparently GATK now uses * to represent long “upstream deletions.”
>
> It looks like as of v82, VEP cannot handle annotation of * alleles. The
> lines in the resulting VCF completely lack VEP’s CSQ field.
>
>
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