Filtering options or tool

[timothymillar]

Consider options or separate tool for filtering based on reported metrics.

Add filtering options to existing tools:

• Simpler as less double handling of values
• Adds additional complexity to complex programs
• Would probably result in running program twice (once with filters and once without)

New filtering tool:

• Double handling of values, filtering a genotype/allele requires updating counts/freqs in other fields
• Would need to be specific to MCHap reported values
• Complexity is isolated to new tool

[timothymillar]

Sort of related to #155, although that could be handled separately to genotype filtering.