Can you please provide
a) GATK version used

4.1.4.1

b) Exact GATK commands used:

gatk HaplotypeCaller --native-pair-hmm-threads 4 -I {sortedBamFile} -R {refFasta} -L {bedFile} -O {vcfFile} --output-mode EMIT_ALL_CONFIDENT_SITES --ERC BP_RESOLUTION

c) The entire error log if applicable:

[14:55:50 INF] Calling variants: /mnt/lab_share/... | /mnt/lab_share/...
Using GATK jar /home/.../gatk-4.1.4.1/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/.../gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar HaplotypeCaller --native-pair-hmm-threads 4 -I /mnt/lab_share/... -R /mnt/lab_share/.../ref/hs38DH.fa -L /mnt/lab_share/... -O /mnt/lab_share/...-gatk.vcf --output-mode EMIT_ALL_CONFIDENT_SITES --ERC BP_RESOLUTION
14:55:52.771 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/.../gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Feb 24, 2020 2:55:52 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
14:55:53.000 INFO HaplotypeCaller - ------------------------------------------------------------
14:55:53.001 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.1.4.1
14:55:53.001 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
14:55:53.001 INFO HaplotypeCaller - Executing as ... on Linux v4.1.12-124.35.1.el7uek.x86_64 amd64
14:55:53.001 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_241-b07
14:55:53.001 INFO HaplotypeCaller - Start Date/Time: February 24, 2020 2:55:52 PM CST
14:55:53.001 INFO HaplotypeCaller - ------------------------------------------------------------
14:55:53.001 INFO HaplotypeCaller - ------------------------------------------------------------
14:55:53.002 INFO HaplotypeCaller - HTSJDK Version: 2.21.0
14:55:53.002 INFO HaplotypeCaller - Picard Version: 2.21.2
14:55:53.002 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:55:53.002 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:55:53.002 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:55:53.002 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:55:53.002 INFO HaplotypeCaller - Deflater: IntelDeflater
14:55:53.002 INFO HaplotypeCaller - Inflater: IntelInflater
14:55:53.002 INFO HaplotypeCaller - GCS max retries/reopens: 20
14:55:53.002 INFO HaplotypeCaller - Requester pays: disabled
14:55:53.002 INFO HaplotypeCaller - Initializing engine
14:55:53.761 INFO FeatureManager - Using codec BEDCodec to read file file:///mnt/lab_share/...
14:55:53.785 INFO IntervalArgumentCollection - Processing 22 bp from intervals
14:55:53.803 INFO HaplotypeCaller - Done initializing engine
14:55:53.805 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
14:55:53.901 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
14:55:53.902 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
14:55:53.915 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/.../gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
14:55:53.919 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/.../gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
14:55:53.973 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
14:55:53.973 INFO IntelPairHmm - Available threads: 4
14:55:53.973 INFO IntelPairHmm - Requested threads: 4
14:55:53.973 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
14:55:54.037 INFO ProgressMeter - Starting traversal
14:55:54.038 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
14:55:54.975 WARN InbreedingCoeff - InbreedingCoeff will not be calculated; at least 10 samples must have called genotypes
14:55:58.306 INFO HaplotypeCaller - 30 read(s) filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
30 read(s) filtered by: (((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter)
30 read(s) filtered by: ((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter)
30 read(s) filtered by: (((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
30 read(s) filtered by: ((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter)
30 read(s) filtered by: (((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter)
29 read(s) filtered by: ((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter)
29 read(s) filtered by: (MappingQualityReadFilter AND MappingQualityAvailableReadFilter)
29 read(s) filtered by: MappingQualityReadFilter
1 read(s) filtered by: NotSecondaryAlignmentReadFilter

14:55:58.306 INFO ProgressMeter - chr22:35380679 0.1 22 309.3
14:55:58.306 INFO ProgressMeter - Traversal complete. Processed 22 total regions in 0.1 minutes.
14:55:58.511 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005727958
14:55:58.511 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.18370724800000002
14:55:58.511 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.01 sec
14:55:58.513 INFO HaplotypeCaller - Shutting down engine
[February 24, 2020 2:55:58 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=403701760

First off, I am very new to all of this and searched for previous posts that may contain my issue and a solution, but I was unable to find anything. In short, my issue is that the .vcf files I am producing will sometimes have a line where there are no supporting reads (DP = 0) but GATK has called the genotype as REF/REF (GT = 0/0). See example line from one of my files:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 
chr1 109690516 . G <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:0,0:0:0:0,0,0

Based on what I read in The Variant Call Format (VCF) Version 4.2 Specification (https://samtools.github.io/hts-specs/VCFv4.2.pdf), "If a call cannot be made for a sample at a given locus, ‘.’ should be specified for each missing allele in the GT field (for example ‘./.’ for a diploid genotype and ‘.’ for haploid genotype)." So, my question is, why is the output for my example being expressed as 0/0 when I would think it should be ./.?

Thanks in advance,

Jeff