Feature request: add annotations and germline calls to mutect calling

[berntpopp]

Follwing command line options could be interesring to add:

--genotype-germline-sites <Boolean>
                              Call all apparent germline site even though they will ultimately be filtered.  Default
                              value: false. Possible values: {true, false}

--genotype-pon-sites <Boolean>Call sites in the PoN even though they will ultimately be filtered.  Default value: false.
                              Possible values: {true, false}

--annotation,-A <String>      One or more specific annotations to add to variant calls  This argument may be specified 0
                              or more times. Default value: null. Possible values: {AlleleFraction, AllelePseudoDepth,
                              AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff,
                              AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality,
                              AS_StrandBiasMutectAnnotation, AS_StrandOddsRatio, AssemblyComplexity, BaseQuality,
                              BaseQualityHistogram, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest,
                              CountNs, Coverage, CycleSkipStatus, DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet,
                              FeaturizedReadSets, FisherStrand, FragmentDepthPerAlleleBySample, FragmentLength,
                              GcContent, GenotypeSummaries, HaplotypeFilteringAnnotation, HmerIndelLength, HmerIndelNuc,
                              HmerMotifs, InbreedingCoeff, IndelClassify, IndelLength, LikelihoodRankSumTest,
                              MappingQuality, MappingQualityRankSumTest, MappingQualityZero, OrientationBiasReadCounts,
                              OriginalAlignment, PossibleDeNovo, QualByDepth, RawGtCount, ReadPosition,
                              ReadPosRankSumTest, ReferenceBases, RMSMappingQuality, SampleList, StrandBiasBySample,
                              StrandOddsRatio, TandemRepeat, UniqueAltReadCount, VariantType}

--annotation-group,-G <String>One or more groups of annotations to apply to variant calls  This argument may be
                              specified 0 or more times. Default value: null. Possible values:
                              {AlleleSpecificAnnotation, AS_StandardAnnotation, GenotypeAnnotation, InfoFieldAnnotation,
                              JumboGenotypeAnnotation, JumboInfoAnnotation, ReducibleAnnotation, StandardAnnotation,
                              StandardFlowBasedAnnotation, StandardHCAnnotation, StandardMutectAnnotation,
                              VariantAnnotation}