samtools (or other tools) to find larger indels

[waalkes]

I am trying to find larger indels across four subspecies. I have a lot of reference contigs from closely related species (~x300 coverage) and ~5x coverage for each of the four subspecies(paired 101bp reads). I used bwa to create .sam files for all the subspecies and samtools seems to work well finding SNPs and small indels but I am at a loss to figure out how to find the larger indels.

Any help?

Thanks.