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

Command to Create VCF:

home/hp/Desktop/GenomicsApps/gatk*/gatk Mutect2 -R /home/hp/Desktop/reference_genome/hg38/hg38.fa -I /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_no_dup_bam/84-B.pon.no-dup.bam  -O /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/84-B.subPoN.vcf.gz

/home/hp/Desktop/GenomicsApps/gatk*/gatk Mutect2 -R /home/hp/Desktop/reference_genome/hg38/hg38.fa -I /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_no_dup_bam/85-B.pon.no-dup.bam  -O /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/85-B.subPoN.vcf.gz

/home/hp/Desktop/GenomicsApps/gatk*/gatk Mutect2 -R /home/hp/Desktop/reference_genome/hg38/hg38.fa  -I /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_no_dup_bam/86-B.pon.no-dup.bam  -O /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/86-B.subPoN.vcf.gz

/home/hp/Desktop/GenomicsApps/gatk*/gatk Mutect2 -R /home/hp/Desktop/reference_genome/hg38/hg38.fa -I /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_no_dup_bam/88-B.pon.no-dup.bam  -O /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/88-B.subPoN.vcf.gz

Command to create PON:

/home/hp/Desktop/GenomicsApps/gatk*/gatk GenomicsDBImport -R /home/hp/Desktop/reference_genome/hg38/hg38.fa  -L /home/hp/Desktop/reference_genome/hg38/hg38.genome.interval_list --genomicsdb-workspace-path /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/PoN_db \

-V /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/84-B.subPoN.vcf.gz\

-V /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/85-B.subPoN.vcf.gz\

-V /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/86-B.subPoN.vcf.gz\

-V /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/88-B.subPoN.vcf.gz

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 -jar /home/hp/Desktop/GenomicsApps/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar GenomicsDBImport -R /home/hp/Desktop/reference_genome/hg38/hg38.fa -L /home/hp/Desktop/reference_genome/hg38/hg38.genome.interval_list --genomicsdb-workspace-path /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/PoN_db -V /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/84-B.subPoN.vcf.gz -V /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/85-B.subPoN.vcf.gz -V /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/86-B.subPoN.vcf.gz -V /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/88-B.subPoN.vcf.gz
14:02:52.745 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/hp/Desktop/GenomicsApps/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:02:52.916 INFO  GenomicsDBImport - ------------------------------------------------------------
14:02:52.916 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.3.0.0
14:02:52.916 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
14:02:52.916 INFO  GenomicsDBImport - Executing as hp@HP-Z8-G4-Workstation on Linux v5.15.0-47-generic amd64
14:02:52.916 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v11.0.16+8-post-Ubuntu-0ubuntu122.04
14:02:52.917 INFO  GenomicsDBImport - Start Date/Time: 2 November 2022 at 2:02:52 PM IST
14:02:52.917 INFO  GenomicsDBImport - ------------------------------------------------------------
14:02:52.917 INFO  GenomicsDBImport - ------------------------------------------------------------
14:02:52.917 INFO  GenomicsDBImport - HTSJDK Version: 3.0.1
14:02:52.918 INFO  GenomicsDBImport - Picard Version: 2.27.5
14:02:52.918 INFO  GenomicsDBImport - Built for Spark Version: 2.4.5
14:02:52.918 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:02:52.918 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:02:52.918 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:02:52.918 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:02:52.918 INFO  GenomicsDBImport - Deflater: IntelDeflater
14:02:52.918 INFO  GenomicsDBImport - Inflater: IntelInflater
14:02:52.918 INFO  GenomicsDBImport - GCS max retries/reopens: 20
14:02:52.918 INFO  GenomicsDBImport - Requester pays: disabled
14:02:52.918 INFO  GenomicsDBImport - Initializing engine
14:02:52.959 WARN  IntelInflater - Zero Bytes Written : 0
14:02:52.999 WARN  IntelInflater - Zero Bytes Written : 0
14:02:53.024 WARN  IntelInflater - Zero Bytes Written : 0
14:02:53.048 WARN  IntelInflater - Zero Bytes Written : 0
14:02:53.233 INFO  FeatureManager - Using codec IntervalListCodec to read file file:///home/hp/Desktop/reference_genome/hg38/hg38.genome.interval_list
14:02:53.303 INFO  IntervalArgumentCollection - Processing 3044953910 bp from intervals
14:02:53.305 WARN  GenomicsDBImport - A large number of intervals were specified. Using more than 100 intervals in a single import is not recommended and can cause performance to suffer. If GVCF data only exists within those intervals, performance can be improved by aggregating intervals with the merge-input-intervals argument.
14:02:53.342 INFO  GenomicsDBImport - Done initializing engine
14:02:53.624 INFO  GenomicsDBLibLoader - GenomicsDB native library version : 1.4.3-6069e4a
14:02:53.625 INFO  GenomicsDBImport - Vid Map JSON file will be written to /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/PoN_db/vidmap.json
14:02:53.625 INFO  GenomicsDBImport - Callset Map JSON file will be written to /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/PoN_db/callset.json
14:02:53.625 INFO  GenomicsDBImport - Complete VCF Header will be written to /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/PoN_db/vcfheader.vcf
14:02:53.625 INFO  GenomicsDBImport - Importing to workspace - /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/PoN_db
14:02:53.837 WARN  IntelInflater - Zero Bytes Written : 0
14:02:53.850 WARN  IntelInflater - Zero Bytes Written : 0
14:02:53.860 WARN  IntelInflater - Zero Bytes Written : 0
14:02:53.871 WARN  IntelInflater - Zero Bytes Written : 0
14:02:53.874 INFO  GenomicsDBImport - Importing batch 1 with 4 samples
14:02:54.077 INFO  GenomicsDBImport - Shutting down engine
[2 November 2022 at 2:02:54 PM IST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2634022912
***********************************************************************

A USER ERROR has occurred: Bad input: GenomicsDBImport does not support GVCFs with MNPs. MNP found at chr1:8330429 in VCF /home/hp/Desktop/WEAP_output_TEST_Pipeline_TOM/output/PON/pon_vcf/88-B.subPoN.vcf.gz

$ grep 8330429 88-B.subPoN.vcf

chr1    8330429    .    GT    CG,<NON_REF>    .    .    AS_SB_TABLE=0,0|0,0|0,0;DP=2;ECNT=4;MBQ=37,11,0;MFRL=166,166,0;MMQ=60,60,60;MPOS=17,50;POPAF=7.30,7.30;TLOD=-4.257e-02,-4.257e-02    GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB    0|1|2:1,1,0:0.333,0.333:2:0,0,0:0,0,0:0,0,0:0|1:8330429_GT_CG:8330429:0,1,1,0
chr1    8330439    .    G    C,<NON_REF>    .    .    AS_SB_TABLE=0,0|0,0|0,0;DP=2;ECNT=4;MBQ=37,11,0;MFRL=166,166,0;MMQ=60,60,60;MPOS=7,50;POPAF=7.30,7.30;TLOD=-4.257e-02,-4.257e-02    GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB    0|1|2:1,1,0:0.333,0.333:2:0,0,0:0,0,0:0,0,0:0|1:8330429_GT_CG:8330429:0,1,1,0
chr1    8330443    .    T    A,<NON_REF>    .    .    AS_SB_TABLE=0,0|0,0|0,0;DP=2;ECNT=4;MBQ=37,11,0;MFRL=166,166,0;MMQ=60,60,60;MPOS=3,50;POPAF=7.30,7.30;TLOD=-4.257e-02,-4.257e-02    GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB    0|1|2:1,1,0:0.333,0.333:2:0,0,0:0,0,0:0,0,0:0|1:8330429_GT_CG:8330429:0,1,1,0

I am seeking help in this regard.