chapmanb/bcbio-nextgen — pull request #476 by mjafin (2014-06-25 11:01:19+00:00)
Title: Scalpel CHI2 filtering added using bcftools. Common InDels REJECTed by b...

...cftools.

I've done the filtering within scalpel.py instead of vfilter.py because scalpel gets added to mutect calls on the fly.