chapmanb/bcbio-nextgen — pull request #68 by lbeltrame (2013-07-26 15:26:04+00:00)
Title: Initial support for paired variant calling using VarScan

Like the MuTect patch before this, it is *incomplete* and will likely not work. It is being posted for review and guidance, in particular to handle the creation of the intermediate pileups (required) and the joining of the files after the calls are complete (VarScan does indels + SNPs separately).