[ensembl-dev] Incorrect pSyntax calculation for indels

[S Venkata Suresh Kumar]

Hi

It seems VEP fails to calculate pSyntax correct for indel (delins)
variants. For eg. for NM_002168.2:c.1358delAinsTAAAGCGT, calculated
pSyntax (by VEP) HGVSp=NP_002159.2.1:p.X453LeufsextX42, which is incorrect.

corresponding vcf record is:

##fileformat=VCFv4.0			
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE_NAME
chr15	90627498	6	CT	CACGCTTTA	100	PASS	Gene=IDH2	GT:DP	1/1:100

For this VCF record, cSyntax calculation is correct, but not  pSyntax
calculation.

I guess we may have to have more test cases for testing vep script, at
least for delins.

-- 
Regards
vs
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