VCF lines with multiple <CNV:TR> ALT alleles get only annotations for the first ALT allele

[dennishendriksen]

Copied from #1848:

When an input VCF contain lines with multiple CNV:TR ALT alleles VEP only annotates the first one. (no annotations with ALLELE_NUM 2 or higher present). We would expect annotations for each ALT allele.

Example input:

chr22	45795355	.	A	<CNV:TR>,<CNV:TR>	.	PASS	.	GT:SO:REPCN	1/0:SPANNING/SPANNING:110/120

These lines can occur for hetrozygote short tandem repeats

VEP version:111

Issue is still present in VEP 115.2

[likhitha-surapaneni]

Hi @dennishendriksen , thank you for reporting this. We recently provided a fix to this (Ensembl/ensembl-variation#1190) which will be made available in the next release.