I want to call SNPs from mapped reads with mapping quality MAPQ zero（for they are mapping to two homologous regions, so they got MQ=0 by bwa-mem）

I add params `--mapping-quality-threshold-for-genotyping 0 --minimum-mapping-quality 0`, but the variant is not called in gvcf. 

And also, add more params like ` --disable-read-filter MappingQualityAvailableReadFilter  --disable-read-filter MappingQualityReadFilter  --disable-read-filter MappedReadFilter --disable-read-filter NotSecondaryAlignmentReadFilter --disable-read-filter NotDuplicateReadFilter`, the variant is still not called in gvcf.

REQUIRED for all errors and issues:
a) GATK version used: 4.3.0.0
b) Exact command used: 

gatk --java-options "-Xmx30G -XX:ParallelGCThreads=40" HaplotypeCaller -R /data/Database/b37/human_g1k_v37.fasta -L X --native-pair-hmm-threads 40 -ERC GVCF -mbq 0 -O chrXsentieonRecal.g.vcf -I recaled.bam --mapping-quality-threshold-for-genotyping 0 --minimum-mapping-quality 0

c) Entire program log:
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 -Xmx30G -XX:ParallelGCThreads=40 -jar /data/abc/softwares/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar HaplotypeCaller -R /data/Database/b37/human_g1k_v37.fasta -L X --native-pair-hmm-threads 40 -ERC GVCF -mbq 0 -O chrXsentieonRecal.gatk4.3.mmq0.mqtg0.g.vcf -I recaled.bam --mapping-quality-threshold-for-genotyping 0 --minimum-mapping-quality 0
17:06:43.071 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/abc/softwares/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
17:06:43.200 INFO  HaplotypeCaller - ------------------------------------------------------------
17:06:43.200 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.3.0.0
17:06:43.200 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
17:06:43.201 INFO  HaplotypeCaller - Executing as abc@ls on Linux v5.4.0-126-generic amd64
17:06:43.201 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_352-8u352-ga-1~18.04-b08
17:06:43.201 INFO  HaplotypeCaller - Start Date/Time: December 1, 2022 5:06:43 PM CST
17:06:43.201 INFO  HaplotypeCaller - ------------------------------------------------------------
17:06:43.201 INFO  HaplotypeCaller - ------------------------------------------------------------
17:06:43.201 INFO  HaplotypeCaller - HTSJDK Version: 3.0.1
17:06:43.201 INFO  HaplotypeCaller - Picard Version: 2.27.5
17:06:43.201 INFO  HaplotypeCaller - Built for Spark Version: 2.4.5
17:06:43.201 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:06:43.201 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:06:43.201 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:06:43.201 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:06:43.202 INFO  HaplotypeCaller - Deflater: IntelDeflater
17:06:43.202 INFO  HaplotypeCaller - Inflater: IntelInflater
17:06:43.202 INFO  HaplotypeCaller - GCS max retries/reopens: 20
17:06:43.202 INFO  HaplotypeCaller - Requester pays: disabled
17:06:43.202 INFO  HaplotypeCaller - Initializing engine
17:06:43.583 INFO  IntervalArgumentCollection - Processing 155270560 bp from intervals
17:06:43.589 INFO  HaplotypeCaller - Done initializing engine
17:06:43.591 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
17:06:43.601 INFO  HaplotypeCallerEngine - Standard Emitting and Calling confidence set to -0.0 for reference-model confidence output
17:06:43.601 INFO  HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
17:06:43.613 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/data/abc/softwares/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
17:06:43.614 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/data/abc/softwares/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
17:06:43.636 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions
17:06:43.636 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
17:06:43.636 INFO  IntelPairHmm - Available threads: 64
17:06:43.636 INFO  IntelPairHmm - Requested threads: 40
17:06:43.636 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
17:06:43.670 INFO  ProgressMeter - Starting traversal
17:06:43.670 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
17:06:44.723 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position X:165361 and possibly subsequent; at least 10 samples must have called genotypes
17:06:45.493 WARN  DepthPerSampleHC - Annotation will not be calculated at position X:186016 and possibly subsequent; genotype for sample 601681 is not called
17:06:45.493 WARN  StrandBiasBySample - Annotation will not be calculated at position X:186016 and possibly subsequent; genotype for sample 601681 is not called

17:06:55.802 INFO  ProgressMeter -             X:801831              0.2                  3050          15085.3
17:07:06.171 INFO  ProgressMeter -            X:1422128              0.4                  5490          14639.3
17:07:16.173 INFO  ProgressMeter -            X:5330014              0.5                 19490          35979.3
17:07:26.172 INFO  ProgressMeter -           X:11175050              0.7                 39530          55804.4
17:07:36.173 INFO  ProgressMeter -           X:16225361              0.9                 56920          65047.7
17:07:46.173 INFO  ProgressMeter -           X:21833404              1.0                 76240          73186.9
17:07:56.175 INFO  ProgressMeter -           X:27070447              1.2                 94410          78127.0
17:08:06.406 INFO  ProgressMeter -           X:32381934              1.4                112680          81715.3
17:08:16.421 INFO  ProgressMeter -           X:38274455              1.5                132880          85959.2
17:08:26.421 INFO  ProgressMeter -           X:43026485              1.7                149380          87228.3
17:08:36.470 INFO  ProgressMeter -           X:47067390              1.9                163390          86909.6
17:08:46.614 INFO  ProgressMeter -           X:48933669              2.0                170020          82975.0
17:08:56.613 INFO  ProgressMeter -           X:50903846              2.2                176820          79802.6
17:09:06.616 INFO  ProgressMeter -           X:53623681              2.4                186240          78172.2
17:09:16.978 INFO  ProgressMeter -           X:58569445              2.6                203410          79608.4
17:09:26.986 INFO  ProgressMeter -           X:62943964              2.7                218390          80233.4
17:09:36.987 INFO  ProgressMeter -           X:67974098              2.9                235630          81571.9
17:09:47.215 INFO  ProgressMeter -           X:70354035              3.1                243950          79746.1
17:09:57.300 INFO  ProgressMeter -           X:73041737              3.2                253290          78486.8
17:10:07.301 INFO  ProgressMeter -           X:75196904              3.4                260790          76841.9
17:10:17.305 INFO  ProgressMeter -           X:82315425              3.6                285280          80121.7
17:10:27.305 INFO  ProgressMeter -           X:90458838              3.7                313110          84005.6
17:10:37.307 INFO  ProgressMeter -           X:99212422              3.9                343010          88087.9
17:10:47.850 INFO  ProgressMeter -          X:102756788              4.1                355270          87297.1
17:10:57.895 INFO  ProgressMeter -          X:107827716              4.2                372630          87944.9
17:11:07.902 INFO  ProgressMeter -          X:113597336              4.4                392390          89101.2
17:11:17.903 INFO  ProgressMeter -          X:118944390              4.6                410880          89897.6
17:11:27.906 INFO  ProgressMeter -          X:122982260              4.7                424830          89678.3
17:11:37.925 INFO  ProgressMeter -          X:128708919              4.9                444500          90636.0
17:11:48.039 INFO  ProgressMeter -          X:132460716              5.1                457410          90168.8
17:11:58.070 INFO  ProgressMeter -          X:138871155              5.2                479460          91500.0
17:12:08.071 INFO  ProgressMeter -          X:146204901              5.4                504610          93331.1
17:12:18.073 INFO  ProgressMeter -          X:151406204              5.6                522480          93745.6
17:12:28.120 INFO  ProgressMeter -          X:153128361              5.7                528420          92045.9
17:12:38.122 INFO  ProgressMeter -          X:153616003              5.9                530210          89751.5
17:12:47.636 INFO  HaplotypeCaller - 0 read(s) filtered by: MappingQualityReadFilter 
0 read(s) filtered by: MappingQualityAvailableReadFilter 
1578 read(s) filtered by: MappedReadFilter 
0 read(s) filtered by: NotSecondaryAlignmentReadFilter 
310165 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 
311743 total reads filtered
17:12:47.636 INFO  ProgressMeter -          X:155270531              6.1                536020          88363.2
17:12:47.636 INFO  ProgressMeter - Traversal complete. Processed 536020 total regions in 6.1 minutes.
17:12:47.653 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.17919341500000002
17:12:47.653 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 11.405189039000001
17:12:47.653 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 58.62 sec
17:12:47.655 INFO  HaplotypeCaller - Shutting down engine
[December 1, 2022 5:12:47 PM CST] org.broadinstitute.h