Update Mutect2 pon WDL

[davidbenjamin]

@takutosato I forgot to deprecate the old orientation bias model in the pon wdl. I also forgot to compile mutect2.pdf from the LaTeX source in a recent PR.

[codecov-io]

Codecov Report

Merging #5859 into master will decrease coverage by 0.135%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #5859       +/-   ##
===============================================
- Coverage     87.061%   86.926%   -0.135%     
- Complexity     32222     32679      +457     
===============================================
  Files           1985      1985               
  Lines         147611    149171     +1560     
  Branches       16230     16603      +373     
===============================================
+ Hits          128512    129669     +1157     
- Misses         13171     13525      +354     
- Partials        5928      5977       +49

Impacted Files	Coverage Δ	Complexity Δ
...lkers/mutect/filtering/GermlineFilterUnitTest.java	57.895% <0%> (-42.105%)	4% <0%> (+1%)
...er/tools/walkers/mutect/Mutect2EngineUnitTest.java	71.875% <0%> (-28.125%)	2% <0%> (-3%)
...titute/hellbender/tools/walkers/GenotypeGVCFs.java	65.625% <0%> (-25.246%)	101% <0%> (-1%)
...ender/utils/variant/writers/TLODBlockUnitTest.java	70.313% <0%> (-23.166%)	7% <0%> (-2%)
...ils/variant/writers/SomaticGVCFWriterUnitTest.java	60.92% <0%> (-16.353%)	3% <0%> (-2%)
...lkers/mutect/SomaticLikelihoodsEngineUnitTest.java	85.366% <0%> (-14.634%)	6% <0%> (ø)
.../broadinstitute/hellbender/utils/QualityUtils.java	71.212% <0%> (-14.154%)	20% <0%> (+6%)
...org/broadinstitute/hellbender/utils/MathUtils.java	67.557% <0%> (-13.761%)	288% <0%> (+77%)
...oadinstitute/hellbender/utils/NaturalLogUtils.java	75% <0%> (-2.778%)	19% <0%> (-1%)
...tools/walkers/mutect/SomaticLikelihoodsEngine.java	91.045% <0%> (-1.978%)	30% <0%> (+12%)
... and 21 more