snp-sites do not see do deletion events about snp-sites

[stitam]

Hi,

I may have come across the same problem, I think snp-sites does not recognise the "-" character, for example:

seq1
ATGAAAATTGGATT
seq2
ATGAAA-TTGGATT

snp-sites -v -o test.vcf test.aln

Here there is a deletion in position 7 in seq2, but snp-sites will not record it. Note, if I replace "-" with any other character e.g. "*", snp-sites will find the site. I am using the docker from staphb (https://hub.docker.com/r/staphb/snp-sites) which contains snp-sites v2.5.1.

I am wondering though, is this behaviour intended? Thanks.