The VCF will have all of this information. One way to summarize all of your data would be to use grep to thin your VCF down to just indels, then read the (tab delimited) result into R and plot whatever you want. Note that, per record, you'll have a chromosome, start position, and stop position, which should give you everything you'll need. Other tools might be able to handle this, but it's just basic text parsing to get what you want.