chapmanb/bcbio-nextgen — pull request #393 by mjafin (2014-04-09 08:54:41+00:00)
Title: FreeBayes paired calling AF thr set to 0.1. Enabled min AF setting in Va...

...rScan paired calling.

As per https://github.com/chapmanb/bcbio-nextgen/pull/392 FreeBayes default minimum AF set to 10%. Enabled using the setting in VarScan paired calling too.

Didn't touch VarScan single sample calling, as the documentation is confusing regarding what the default is. The help shows 1% minimum AF but actually running VarScan shows 20%.