Scramble sensitivity tuning

[mwalker174]

Suggested by @cwhelan in #722, hard filtering in the Scramble is performed in GatherSampleEvidence, which may not be desirable for some users. While users can tune filtering cutoffs when running calling, they cannot do so post hoc. Lowering the default threshold fed to Scramble and then filtering with a higher threshold when creating the VCF would at least permit sensitivity analysis from the table output without having to re-run the tool.

Note that one drawback to loosening filtering criteria is that it may substantially increase wall time, as consensus sequence alignment is expensive.