REQUIRED for all errors and issues:
a) GATK version used: 4.3.0
b) Exact command used:

java -Xmx6g -jar gatk-package-4.3.0.0-local.jar HaplotypeCaller   -R hg19.fa -L dummy.bed -mbq 15  -G StandardAnnotation --standard-min-confidence-threshold-for-calling 25 --disable-read-filter NotDuplicateReadFilter --kmer-size 30  --max-reads-per-alignment-start 0 -I dummy.bam -O dummy.vcf --dont-use-soft-clipped-bases

This command leads to a spurios confident indel call  at position chr2:21225268. There is no evidence of this indel at all when looking at the reads (only 4 reads out of thousands have it). Removing "mbq 15" parameters removes the call (but this filter is important for other calls). Removing "kmer-size 30" also removes the indel call, but also removes the real SNP call at chr2:21225281.

I uploaded the data to: ulitsky_Jan25_2025.zip

c) Entire program log:

17:23:27.138 WARN  GATKAnnotationPluginDescriptor - Redundant enabled annotation group (StandardAnnotation) is enabled for this tool by default

17:23:27.174 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/labs/ulitsky/igoru/gatk/gatk4/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

17:23:27.258 INFO  HaplotypeCaller - ------------------------------------------------------------

17:23:27.259 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.3.0.0

17:23:27.259 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/

17:23:27.259 INFO  HaplotypeCaller - Executing as igoru@login3.wexac.weizmann.ac.il on Linux v5.14.0-162.6.1.el9_1.x86_64 amd64

17:23:27.259 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.20+8

17:23:27.259 INFO  HaplotypeCaller - Start Date/Time: January 25, 2025 at 5:23:27 PM IST

17:23:27.259 INFO  HaplotypeCaller - ------------------------------------------------------------

17:23:27.259 INFO  HaplotypeCaller - ------------------------------------------------------------

17:23:27.260 INFO  HaplotypeCaller - HTSJDK Version: 3.0.1

17:23:27.260 INFO  HaplotypeCaller - Picard Version: 2.27.5

17:23:27.260 INFO  HaplotypeCaller - Built for Spark Version: 2.4.5

17:23:27.260 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2

17:23:27.260 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

17:23:27.260 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

17:23:27.260 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

17:23:27.260 INFO  HaplotypeCaller - Deflater: IntelDeflater

17:23:27.260 INFO  HaplotypeCaller - Inflater: IntelInflater

17:23:27.260 INFO  HaplotypeCaller - GCS max retries/reopens: 20

17:23:27.260 INFO  HaplotypeCaller - Requester pays: disabled

17:23:27.260 INFO  HaplotypeCaller - Initializing engine

17:23:27.368 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/labs/ulitsky/igoru/gatk/wildmix/dummy.bed

17:23:27.372 INFO  IntervalArgumentCollection - Processing 200 bp from intervals

17:23:27.375 INFO  HaplotypeCaller - Done initializing engine

17:23:27.383 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output

17:23:27.392 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/labs/ulitsky/igoru/gatk/gatk4/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so

17:23:27.394 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/labs/ulitsky/igoru/gatk/gatk4/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so

17:23:27.405 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions

17:23:27.405 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM

17:23:27.405 INFO  IntelPairHmm - Available threads: 256

17:23:27.406 INFO  IntelPairHmm - Requested threads: 4

17:23:27.406 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation

17:23:27.423 INFO  ProgressMeter - Starting traversal

17:23:27.423 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute

17:23:30.057 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position chr2:21225268 and possibly subsequent; at least 10 samples must have called genotypes

17:23:30.100 INFO  HaplotypeCaller - 1 read(s) filtered by: MappingQualityReadFilter

0 read(s) filtered by: MappingQualityAvailableReadFilter

0 read(s) filtered by: MappedReadFilter

0 read(s) filtered by: NotSecondaryAlignmentReadFilter

0 read(s) filtered by: PassesVendorQualityCheckReadFilter

0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter

0 read(s) filtered by: GoodCigarReadFilter

0 read(s) filtered by: WellformedReadFilter

1 total reads filtered

17:23:30.100 INFO  ProgressMeter -             unmapped              0.0                     3             67.2

17:23:30.100 INFO  ProgressMeter - Traversal complete. Processed 3 total regions in 0.0 minutes.

17:23:30.111 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015311268000000001

17:23:30.111 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.8879550620000001

17:23:30.111 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.54 sec

17:23:30.112 INFO  HaplotypeCaller - Shutting down engine

[January 25, 2025 at 5:23:30 PM IST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.05 minutes.