How to merge indels

I'm calling variants from 10 samples using one reference fasta for all. The samples are from the same strain. One sample is WT and the others were under different stress selection. The purpose is to find out whether the stress brought any mutations and what they are.

In order to do this, I need to merge the variant calling results from all samples. For example, if a position is 0/0 in the WT sample, but 1/1 in one of the stressed samples this would be of our interest.

Ideally I would want to do a joint calling from all samples together. But Snippy can only call each sample individually and it only outputs variants so all 0/0 sites are lost. I know I can use snippy-core to merge SNPs to get those 0/0 sites back, but it does not handle indels.

My questions are: (1) Is it possible to let snippy output all callable sites including 0/0? Or (2) Is it possible to let snippy-core output all variants including indels?

Any other solution?

Thanks,