If you have symbolic variants with the same chrom/pos/ref/alt but different SVLEN, they are treated as identical, meaning you silently drop symbolic variants

Example VCF:

##fileformat=VCFv4.1
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
NC_000012.11	88520131	23651	C	<DEL>	.	.	SVLEN=-1000;SVTYPE=DEL
NC_000012.11	88520131	24042	C	<DEL>	.	.	SVLEN=-2000;SVTYPE=DEL
NC_000012.11	88520131	24043	C	<DEL>	.	.	SVLEN=-3000;SVTYPE=DEL

These are different variants (1k, 2k, 3k deletions) and are not unique.

Ideally, vt would take into account SVLEN

At the least - if you see a symbolic alt, you should perhaps write a warning to STDERR saying that symbolic variants are not treated correctly, and will be removed