Adding indels in `core.vcf`

[davidtong28]

Greetings!

Thank you for developing Snippy! I'm a big fan of it. I recently noticed some interesting indels in my sequences. Snippy is able to detect them and store them to snps.vcf. However I noticed that after running snippy_core, core.vcf does not contain indel informations anymore. I understand that indels can be hard to (and not useful) incorperate in generating core.aln, so I'm wondering if there is a way to summarize all the detected indels using snippy_core.

Sincerely,

David