variant filtering parameter cleanup

[malachig]

This PR is related to issue https://github.com/wustl-oncology/analysis-wdls/issues/97 and is a competing PR with https://github.com/wustl-oncology/analysis-wdls/pull/104 by @Layth17.

The purpose is to:

• simplifying the specification of defaults for variant frequency and llr cutoffs throughout the pipeline. Confining the setting of defaults to the tool itself (and allowing override in a YAML by any pipeline that uses that tool).
• clarify variable names to make it more clear how varscan min_freq cutoffs are used compared to those used by fp_filter for strelka, mutect and pindel
• make sure that the varscan min_freq parameters are independent of those specified for strelka, mutect and pindel

[malachig]

Working on testing but if all goes well this PR should be deprecated by:

https://github.com/wustl-oncology/analysis-wdls/pull/136

[malachig]

Testing of #136 worked out. Closing this PR.