[ensembl-dev] complex variant effect predition

[Bram De Wilde]

Hi everyone,

While unraveling the complex variants that can be encoded in the vcf format (http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-40) I came to realize that I don't know how to submit some of these complex alleles to the ensembl variation API for effect prediction.
For simple SNP's and indels the situation is clearly described in the help pages. The problem I seem to be having is with complex alleles:

eg. when a SNP is directly followed by an deletion on a chromosome z
ref:	ACGTAGA
var:	ACA--GA

this can be encoded as 2 variants:
chr	start		stop		variant	strand
z	3	3	G/A		+
z	4	5	TA/-		+
but clearly none of these  will have the functional consequence of the true allele namely:
z	3	5	GTA/A	+
unfortunately this kind of allele does not seem to return any response from the variation API

I can think of a simmilar situation for an insertion:
ref:	ACG-TAGA
var:	ACACTAGA

where:
chr	start		stop		variant	strand
z	3	3	G/A		+
z	4	3	-/C		+
will not have the same consequence as
z	4	3	G/AC	+


Or do I see this all wrong?
is there a way to submit alleles like these for effect prediction?


Kind regards,


Bram De Wilde, MD
Center for Medical Genetics Ghent (CMGG)
Ghent University Hospital
Medical Research Building (MRB), 2nd floor, room 120.050
De Pintelaan 185, B-9000 Ghent, Belgium
+32 9 332 4812 (phone) | +32 9 332 6549 (fax)
http://medgen.ugent.be/
Bram.DeWilde at UGent.be 



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