REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

/usr/bin/time -v ${GATK} \
  HaplotypeCaller \
  -R $ref_fa \
  -I $File \
  -L targets.bed \
  --dont-use-soft-clipped-bases \
  -O ${output} \
  -bamout $bamout \
  -stand-call-conf 20 > $sample.log 2>&1
 
c) Entire program log:

Using GATK jar /work/opt/ohpc/Taiwania3/pkg/biology/GATK/gatk_v4.2.0.0/gatk-package-4.2.0.0-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 /work/opt/ohpc/Taiwania3/pkg/biology/GATK/gatk_v4.2.0.0/gatk-package-4.2.0.0-local.jar HaplotypeCaller -R /staging/biology/v00hcc00/Routine/1.SequenceSource/Reference/human_g1k_v37_Add_chr.fa -I /staging/biology/v00hcc00/joseph_test/220411552_S47_L001_merged.bam -L targets.bed --dont-use-soft-clipped-bases -O /staging/biology/v00hcc00/joseph_test/220402252_S45_L001_merged_target.vcf.gz -bamout /staging/biology/v00hcc00/joseph_test/220402252_S45_L001_merged_target.out.bam -stand-call-conf 20
16:24:05.577 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/work/opt/ohpc/Taiwania3/pkg/biology/GATK/gatk_v4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Nov 25, 2022 4:24:05 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
16:24:05.700 INFO  HaplotypeCaller - ------------------------------------------------------------
16:24:05.701 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.0.0
16:24:05.701 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
16:24:05.701 INFO  HaplotypeCaller - Executing as v00hcc00@lgn304 on Linux v3.10.0-1127.el7.x86_64 amd64
16:24:05.701 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-b08
16:24:05.701 INFO  HaplotypeCaller - Start Date/Time: November 25, 2022 4:24:05 PM CST
16:24:05.701 INFO  HaplotypeCaller - ------------------------------------------------------------
16:24:05.701 INFO  HaplotypeCaller - ------------------------------------------------------------
16:24:05.702 INFO  HaplotypeCaller - HTSJDK Version: 2.24.0
16:24:05.702 INFO  HaplotypeCaller - Picard Version: 2.25.0
16:24:05.702 INFO  HaplotypeCaller - Built for Spark Version: 2.4.5
16:24:05.702 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:24:05.702 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:24:05.702 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:24:05.702 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:24:05.702 INFO  HaplotypeCaller - Deflater: IntelDeflater
16:24:05.702 INFO  HaplotypeCaller - Inflater: IntelInflater
16:24:05.702 INFO  HaplotypeCaller - GCS max retries/reopens: 20
16:24:05.702 INFO  HaplotypeCaller - Requester pays: disabled
16:24:05.702 INFO  HaplotypeCaller - Initializing engine
16:24:06.178 INFO  FeatureManager - Using codec BEDCodec to read file file:///staging/biology/v00hcc00/joseph_test/targets.bed
16:24:06.185 INFO  IntervalArgumentCollection - Processing 5258 bp from intervals
16:24:06.192 INFO  HaplotypeCaller - Done initializing engine
16:24:06.200 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
16:24:06.242 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/work/opt/ohpc/Taiwania3/pkg/biology/GATK/gatk_v4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
16:24:06.243 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/work/opt/ohpc/Taiwania3/pkg/biology/GATK/gatk_v4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
16:24:06.288 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions
16:24:06.288 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
16:24:06.288 INFO  IntelPairHmm - Available threads: 56
16:24:06.288 INFO  IntelPairHmm - Requested threads: 4
16:24:06.288 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
16:24:06.310 INFO  ProgressMeter - Starting traversal
16:24:06.310 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
16:24:07.584 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position chr4:41748007 and possibly subsequent; at least 10 samples must have called genotypes
16:24:10.011 INFO  HaplotypeCaller - 7 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: NotDuplicateReadFilter 
0 read(s) filtered by: PassesVendorQualityCheckReadFilter 
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter 
0 read(s) filtered by: GoodCigarReadFilter 
0 read(s) filtered by: WellformedReadFilter 
7 total reads filtered
16:24:10.011 INFO  ProgressMeter -            chrM:1401              0.1                    41            664.7
16:24:10.011 INFO  ProgressMeter - Traversal complete. Processed 41 total regions in 0.1 minutes.
16:24:10.020 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.003949149
16:24:10.020 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.331429817
16:24:10.020 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 1.52 sec
16:24:10.087 INFO  HaplotypeCaller - Shutting down engine
[November 25, 2022 4:24:10 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=2532835328
    Command being timed: "/opt/ohpc/Taiwania3/pkg/biology/GATK/gatk_v4.2.0.0/gatk HaplotypeCaller -R /staging/biology/v00hcc00/Routine/1.SequenceSource/Reference/human_g1k_v37_Add_chr.fa -I /staging/biology/v00hcc00/joseph_test/220411552_S47_L001_merged.bam -L targets.bed --dont-use-soft-clipped-bases -O /staging/biology/v00hcc00/joseph_test/220402252_S45_L001_merged_target.vcf.gz -bamout /staging/biology/v00hcc00/joseph_test/220402252_S45_L001_merged_target.out.bam -stand-call-conf 20"
    User time (seconds): 23.14
    System time (seconds): 2.03
    Percent of CPU this job got: 328%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.66
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 1300260
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 0
    Minor (reclaiming a frame) page faults: 543803
    Voluntary context switches: 42415
    Involuntary context switches: 333
    Swaps: 0
    File system inputs: 0
    File system outputs: 5424
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0
 

Hello,

There are two samples with the same panel. Section 2 and section 4 are the bamout of each sample. There is a deletion in the red box. My question is why the red box in sample 2 is not considered in the active region, but sample 1 is been. The active region let me lose the deletion. Any solution to solve it without --force command because my panel is not small? Then, I can still output the deletion.

Thanks