Add citations for GATK2, MACS2, and bedtools.

These are just for the main papers, we had talked in e-mail about URL based citations in particular for bedtools. I have not included that here but one could add BibTeX entries for those URLs and I have updated the Citations Future Work Trello card with an idea to make this easier (https://trello.com/c/R8vKH4PQ).

Note in the code about MACS2 paper - for some reason dx.doi.org cannot build a BibTeX entry for it - so citation is annotated using BibTeX instead of a DOI.