Update Mutect2 javadoc to reflect v4.1 changes

[sooheelee]

- Running in mitochonrial mode
- Link to liquid biopsy blogpost will need to be added once it is posted
- Specifying tumor name is no longer necessary
- Af-of-alleles-not-in-resource is dynamically adjusted for modes
- Joint calling on multiple tumor and normal samples
- Mention and/or link to FilterMutectCalls, Funcotator and CreateSomaticPanelOfNormals
- Remove caveat and state instead M2's ability to handle extreme high depths
- Update HaplotypeCaller link from v3 to current
- Add 'Notes' section and make ordered list
- Move example AF resource snippet to 'Notes' section

[sooheelee]

@davidbenjamin here is the PR to the documentation updates we have been working on. I made a few additional stylistic changes, fyi.

[davidbenjamin]

Looks good!

[codecov-io]

Codecov Report

Merging #5769 into master will decrease coverage by 49.877%.
The diff coverage is n/a.

@@               Coverage Diff                @@
##              master     #5769        +/-   ##
================================================
- Coverage     86.982%   37.105%   -49.877%     
+ Complexity     31861     17674     -14187     
================================================
  Files           1943      1943                
  Lines         146770    146770                
  Branches       16223     16223                
================================================
- Hits          127663     54459     -73204     
- Misses         13194     87399     +74205     
+ Partials        5913      4912      -1001

Impacted Files	Coverage Δ	Complexity Δ
...itute/hellbender/tools/walkers/mutect/Mutect2.java	84.091% <ø> (ø)	22 <0> (ø)	⬇️
...ls/variant/writers/GVCFBlockCombiningIterator.java	0% <0%> (-100%)	0% <0%> (-1%)
...ls/walkers/genotyper/HeterogeneousPloidyModel.java	0% <0%> (-100%)	0% <0%> (-14%)
...nder/utils/downsampling/FractionalDownsampler.java	0% <0%> (-100%)	0% <0%> (-17%)
...park/pathseq/MarkedOpticalDuplicateReadFilter.java	0% <0%> (-100%)	0% <0%> (-4%)
...otypecaller/RandomLikelihoodCalculationEngine.java	0% <0%> (-100%)	0% <0%> (-6%)
...r/utils/solver/UnivariateSolverSpecifications.java	0% <0%> (-100%)	0% <0%> (-4%)
...ute/hellbender/utils/hmm/UninformativeTestHMM.java	0% <0%> (-100%)	0% <0%> (-5%)
...ender/utils/svd/OjAlgoSingularValueDecomposer.java	0% <0%> (-100%)	0% <0%> (-3%)
...typer/afcalc/OriginalDiploidExactAFCalculator.java	0% <0%> (-100%)	0% <0%> (-15%)
... and 1222 more

[sooheelee]

Awesome. Thanks David. This is merged and closed now.