Hi,

Thanks a lot for this tool.

I am using it to perform a liftover from hg38 to hg19 on a VCF file. I have tried different target genome assemblies for hg19, but the output VCF still has the same chromosomal positions as the input. The command I’m using is:

CrossMap vcf --chromid s --compress hg38ToHg19.over.chain.gz CHR_ALL.RS.annotated.filtered.vcf.gz ucsc.hg19.fasta CHR_ALL.RS.annotated.filtered.hg19.vcf.gz

I get no errors, but the chromosomal positions are not changed.

Thank you,
Arianna