Issue title: freebayes calls SNP instead of INDEL
 Issue body: Hello,
in my reference sequence there is a pattern 11 times TG followed by 7 times T. Now I have a sample which I already sequenced by sanger resulting in one allel with 11xTG/5xT and one with 12xTG/7xT.

If I have a look at the alignment file for my NGS analysis I can guess the same result. But freebayes says there are 11/12xTG (which is ok) and a SNP T>G which is not the same as a 2bp deletion. In contrast gatk's HaplotypeCaller have the correct result.

I don't understand what freebayes is doing here. Are there any parameters with which I can influence the result. 

In the attachment you can see the relevant position in igv. What more information can I provide to you?

Thanks a lot.

fin swimmer

![cftr](https://cloud.githubusercontent.com/assets/2164565/22061364/f2de2862-dd74-11e6-8fc4-fb8636faa43a.jpg)

 Comments: 
 Comment 0: This issue is marked stale because it has been open 120 days with no activity. Remove stale label or comment or this will be closed in 5 days
 Comment 1: This issue was closed for lack of activity. Feel free to re-open if someone feels like working on it.
{'source': 'GithubIssues', 'repo_name_with_owner': 'freebayes/freebayes', 'issue_id': 201539876, 'repo_stars': 636.0}