Issue with liftover of vcf file from T2T to hg38

[Taghrid-M]

Dear Crossmap Maintainer,

I am reaching out to report an issue I've encountered while using Crossmap. I was trying to liftover my VCF file from T2T to hg38, but found a significant number of variants were rejected during the process. The total number of rejected variants was around 1,855,261, which is quite a significant figure.

To perform the liftover, I've used both the chain file from github.com/marbl/CHM13 and the UCSC chain file. Unfortunately, the issue persisted with both chain files.

Here is the command line: CrossMap.py vcf $chain_file $input_vcf $GRCh38_REF $output_vcf

I was wondering if you could help me understand why this is happening, and if there's a possible solution or workaround. Perhaps I'm missing something, or there could be an issue with the chain files I've used?

Thank you in advance.

Taghrid