Use bcftools and vcflib for splitting variants into SNPs and Indels and merging samples back together. #294 Clarify and test for correct usage of various merging functions.
Avoid using newer pysam from binstars which causes issues on CentOS. Fixes #319
Improved fix for pysam on CentOS, use up to date pysam package compiled on CentOS 5 from bcbio binstar channel. #319