Remove the -s call as it is too stringent (see issue #314)
Remove the pvar option, let hard filtering do the selection (like germline calling)
Merge pull request #349 from lbeltrame/freebayes-fixes

Miscellaneous fixes for FreeBayes
Add hard vcffilter to FreeBayes tumor calls to remove extremely low quality variants which cause issues with GATK post-processing #349