If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:

gatk-4.1.3.0

b) Exact command used:

java -jar picard.jar LiftoverVcf I=$input_vcf O=$output_vcf CHAIN=$chain REJECT=$reject_vcf R=hg19.fa

c) Entire error log:

INFO    2020-09-28 12:50:33     LiftoverVcf     Loading up the target reference genome.

INFO    2020-09-28 12:50:37     LiftoverVcf     Lifting variants over and sorting.

[Mon Sep 28 12:50:37 EDT 2020] picard.vcf.LiftoverVcf done. Elapsed time: 0.08 minutes.

Runtime.totalMemory()=6855065600

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

Exception in thread "main" java.lang.IllegalStateException: Allele in genotype A not in the variant context [G*, T]

        at htsjdk.variant.variantcontext.VariantContext.validateGenotypes(VariantContext.java:1317)

        at htsjdk.variant.variantcontext.VariantContext.validate(VariantContext.java:1255)

        at htsjdk.variant.variantcontext.VariantContext.<init>(VariantContext.java:392)

        at htsjdk.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:486)

        at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:200)

        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)

        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)

        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

If not an error, choose a category for your question(REQUIRED):
c) Why do I see his error?
My input vcf file using reference build GRCh36, I want to convert it to hg19. So i downloaded the chain file hg18tohg19 from

http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/

To prepare input VCF file, I also added "Chr" to the first chromosome column, otherwise it did not work at all.

For testing, I subset 1000 rows using the command above, and it worked.

But when I used the full VCF file, it returned to me this error. I do not know why it happened. And I want to know whether anyone knows how to fix it?