A band-aid approach is to simply look for overlap in indel calls within a window. Even a tiny window can make a big difference to small indels.
To do this, I currently use VCFtools, which makes it very simple. Specifically, use the vcf-isec command with the -w parameter.
If I compare two libraries sequenced from the same individual that had indels called independently (using the same method), I end up with a few thousand overlapping indels that would have been assessed as independent from one another if I looked for exact overlap.
Overlap +/- 5b:vcf-isec -f -n =2 -o indels1.vcf.gz indels2.vcf.gz | wc -l468136
I realize it's not that astounding a difference, but keep in mind this is looking at two different libraries from the same individual. If you're comparing calls from two completely different sequencing platforms or variant callers, these numbers jump quite a bit.vcf-isec -f -n =2 -o -w 5 indels1.vcf.gz indels2.vcf.gz | wc -l471047