Allow for additional indels VCF

[eriqande]

If we are adding more samples to others that were previously processed I want to be able to merge
newly discovered indels with ones that were found previously in order to do indel realignment.

I should be able to have a config option which is something like:

indel_vcf: ""

If it is empty, then nothing needs to be done. If it is not empty, then we need to merge those indels into the ones
discovered in the current run. Shouldn't be too hard.

I will get on this once I really need it.