[ensembl-dev] VEP cannot annotate * alternate alleles

[JESSICA X. CHONG]

Ahhh ok, this makes sense to find the annotation on the previous line.

Thanks.

On Nov 16, 2015, at 3:00 AM, Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>> wrote:

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<mailto: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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