Hi. I have been migrating our workflow our gatk3 workflow to gatk4 (4.1.4.1) and encountered a strange problem with HaplotypeCaller: The generated index file is larger than the generated g.vcf file. If I regenerate the index using IndexFeatureFile, the generated idx file is much smaller.

The reason I care is that the next step (GenomicsDBImport) is a lot faster (and uses less memory) with the small (regenerated) index files (0.3min vs 1.7 min per batch).

I am using the following command:
```
gatk HaplotypeCaller -R /opt/data/dna/testdata/hg19/ucsc_hg19.fa -I AACGAGAATGGAGCTCAA-1.bam -L ~/results/gatk4-MBM292-8/gatk.bed --emit-ref-confidence BP_RESOLUTION -O AACGAGAATGGAGCTCAA.g.vcf
```

This is its output:
```
Using GATK jar /home/anze/tp4/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/anze/tp4/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar HaplotypeCaller -R /opt/data/dna/testdata/hg19/ucsc_hg19.fa -I AACGAGAATGGAGCTCAA-1.bam -L /home/anze/results/gatk4-MBM292-8/gatk.bed --emit-ref-confidence BP_RESOLUTION -O AACGAGAATGGAGCTCAA.g.vcf
20:14:00.473 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/anze/tp4/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
20:14:00.972 INFO  HaplotypeCaller - ------------------------------------------------------------
20:14:00.974 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.4.1
20:14:00.975 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
20:14:00.980 INFO  HaplotypeCaller - Executing as anze@naringi-instance-rna on Linux v5.0.0-1028-gcp amd64
20:14:00.980 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
20:14:00.980 INFO  HaplotypeCaller - Start Date/Time: February 20, 2020 8:14:00 PM UTC
20:14:00.981 INFO  HaplotypeCaller - ------------------------------------------------------------
20:14:00.981 INFO  HaplotypeCaller - ------------------------------------------------------------
20:14:00.995 INFO  HaplotypeCaller - HTSJDK Version: 2.21.0
20:14:00.995 INFO  HaplotypeCaller - Picard Version: 2.21.2
20:14:00.995 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:14:00.995 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:14:00.996 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:14:00.996 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:14:00.996 INFO  HaplotypeCaller - Deflater: IntelDeflater
20:14:00.997 INFO  HaplotypeCaller - Inflater: IntelInflater
20:14:00.997 INFO  HaplotypeCaller - GCS max retries/reopens: 20
20:14:00.997 INFO  HaplotypeCaller - Requester pays: disabled
20:14:00.997 INFO  HaplotypeCaller - Initializing engine
20:14:01.650 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/anze/results/gatk4-MBM292-8/gatk.bed
20:14:01.671 INFO  IntervalArgumentCollection - Processing 21692 bp from intervals
20:14:01.708 INFO  HaplotypeCaller - Done initializing engine
20:14:01.711 INFO  HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled
20:14:01.735 INFO  HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
20:14:01.735 INFO  HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
20:14:01.794 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/anze/tp4/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
20:14:01.801 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/anze/tp4/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
20:14:01.860 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:14:01.862 INFO  IntelPairHmm - Available threads: 16
20:14:01.862 INFO  IntelPairHmm - Requested threads: 4
20:14:01.862 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:14:01.919 INFO  ProgressMeter - Starting traversal
20:14:01.920 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
20:14:03.240 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated; at least 10 samples must have called genotypes
20:14:12.635 INFO  ProgressMeter -        chr6:44229670              0.2                    80            448.0
20:14:25.251 INFO  ProgressMeter -       chr14:35871924              0.4                   160            411.5
20:14:35.454 INFO  ProgressMeter -        chr19:9072842              0.6                   220            393.6
20:14:41.728 INFO  HaplotypeCaller - No reads filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
20:14:41.735 INFO  ProgressMeter -        chrX:44938526              0.7                   268            403.9
20:14:41.735 INFO  ProgressMeter - Traversal complete. Processed 268 total regions in 0.7 minutes.
20:14:42.047 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.08534575900000001
20:14:42.048 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 6.938380428
20:14:42.048 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 14.11 sec
20:14:42.052 INFO  HaplotypeCaller - Shutting down engine
[February 20, 2020 8:14:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.69 minutes.
Runtime.totalMemory()=1819279360

```

And these are the file sizes created by Haplotype caller:
```
-rw-rw-r-- 1 anze anze 1.6M Feb 20 20:14 AACGAGAATGGAGCTCAA.g.vcf
-rw-rw-r-- 1 anze anze 7.9M Feb 20 20:14 AACGAGAATGGAGCTCAA.g.vcf.idx
```

And file sizes if I regenerate index using 
```
gatk IndexFeatureFile --input AACGAGAATGGAGCTCAA.g.vcf
```
are
```
-rw-rw-r-- 1 anze anze 1.6M Feb 20 20:14 AACGAGAATGGAGCTCAA.g.vcf
-rw-rw-r-- 1 anze anze 128K Feb 20 20:15 AACGAGAATGGAGCTCAA.g.vcf.idx
```