Merge pull request #393 from mjafin/master

FreeBayes paired calling AF thr set to 0.1. Enabled min AF setting in Va...
Use Tophat2 as the default aligner.

We do not install the STAR indices by default, so default to
 Tophat2 since those indices are guaranteed to be there.
Update lumpy to latest recommendations, using samblaster for BAM preparation and speedseq for lumpy integration
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Provide initial support for subsetting variant calls to avoid low complexity regions identified by Heng Li https://github.com/lh3/varcmp/tree/master/scripts http://arxiv.org/abs/1404.0929
Provide initial support for running delly structural variant caller
Correctly handle multiple batch variant callers. Thanks to @dfjenkins3