Papers Describing Indel Calling Algorithms

[ndelaney]

Does anyone happen to know where I could find detailed information on the algorithms used to call indels and assign confidence for the following programs:

* GATK
* SAMTOOLS
* Vardict
* FreeBayes

I gather some of the publications out there are out of date.

[Len Trigg]

If you are interested in the algorithms behind indel calling in general, the method used by RTG Core for indel calling (and complex haplotype calling) is described in: http://www.ncbi.nlm.nih.gov/pubmed/24874280