Dear GATK team, 

I am currently running LiftoverVcf paramter to do a liftover from hg19 to hg38 on the normalize vcf file generated via "GtcToVcf" parameter. Upon running the script, I find out that there is no successful variants were lifted. Thus, I request for your help to look over this issue.

REQUIRED for all errors and issues:
a) GATK version used: Picard version: 3.0.0-1-g62ec81c-SNAPSHOT
b) Exact command used: LiftoverVcf -I 21N10057_normalize.vcf -O 21N10057_normalize_lifted38.vcf -CHAIN /home/user3/Documents/g24_pharmacogenomics/hg19ToHg38.over.chain.gz -REJECT 21N10057_rejected_variants.vcf -R /home/user3/Documents/Human_reference/hg38_reference/hg38.fa
c) Entire program log:

INFO    2024-05-06 11:56:09    LiftoverVcf    

********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** 
https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
**********    LiftoverVcf -I 21N10057_normalize.vcf -O 21N10057_normalize_lifted38.vcf -CHAIN /home/user3/Documents/g24_pharmacogenomics/hg19ToHg38.over.chain.gz -REJECT 21N10057_rejected_variants.vcf -R /home/user3/Documents/Human_reference/hg38_reference/hg38.fa
**********

11:56:09.211 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/user3/Downloads/picard/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon May 06 11:56:09 MYT 2024] LiftoverVcf INPUT=21N10057_normalize.vcf OUTPUT=21N10057_normalize_lifted38.vcf CHAIN=/home/user3/Documents/g24_pharmacogenomics/hg19ToHg38.over.chain.gz REJECT=21N10057_rejected_variants.vcf REFERENCE_SEQUENCE=/home/user3/Documents/Human_reference/hg38_reference/hg38.fa    WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon May 06 11:56:09 MYT 2024] Executing as user3@user3-pc3 on Linux 6.5.0-26-generic amd64; OpenJDK 64-Bit Server VM 17.0.10+7-Ubuntu-122.04.1; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 3.0.0-1-g62ec81c-SNAPSHOT
INFO    2024-05-06 11:56:09    LiftoverVcf    Loading up the target reference genome.
INFO    2024-05-06 11:56:26    LiftoverVcf    Lifting variants over and sorting (not yet writing the output file.)
INFO    2024-05-06 11:56:44    LiftoverVcf    Processed 648050 variants.
INFO    2024-05-06 11:56:44    LiftoverVcf    648050 variants failed to liftover.
INFO    2024-05-06 11:56:44    LiftoverVcf    0 variants lifted over but had mismatching reference alleles after lift over.
INFO    2024-05-06 11:56:44    LiftoverVcf    100.0000% of variants were not successfully lifted over and written to the output.
INFO    2024-05-06 11:56:44    LiftoverVcf    liftover success by source contig:
INFO    2024-05-06 11:56:44    LiftoverVcf    1: 0 / 50670 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    10: 0 / 30882 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    11: 0 / 32264 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    12: 0 / 29644 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    13: 0 / 22056 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    14: 0 / 19634 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    15: 0 / 20076 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    16: 0 / 21786 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    17: 0 / 22417 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    18: 0 / 17387 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    19: 0 / 19164 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    2: 0 / 51635 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    20: 0 / 14662 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    21: 0 / 8958 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    22: 0 / 10131 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    3: 0 / 41867 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    4: 0 / 38034 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    5: 0 / 35354 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    6: 0 / 43191 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    7: 0 / 33758 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    8: 0 / 28490 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    9: 0 / 23928 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    MT: 0 / 903 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    X: 0 / 26711 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    Y: 0 / 4448 (0.0000%)
INFO    2024-05-06 11:56:44    LiftoverVcf    lifted variants by target contig:
INFO    2024-05-06 11:56:44    LiftoverVcf    no successfully lifted variants
WARNING    2024-05-06 11:56:44    LiftoverVcf    0 variants with a swapped REF/ALT were identified, but were not recovered.  See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO    2024-05-06 11:56:44    LiftoverVcf    Writing out sorted records to final VCF.
[Mon May 06 11:56:44 MYT 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.60 minutes.
Runtime.totalMemory()=5553258496
user3@user3-pc3:~/Documents/g24_ph

Thank you