Hi,

I am trying to lift the New York Genome Centre 1000 Genomes 30x on GRCh38 to GRCh37. As this file is a vcf I am trying to use picard's liftOverVCF tool. However, using the UCSC hg38 to hg19 chain file and the above mentioned vcf I get the following output:

INFO    2022-10-27 13:37:40 LiftoverVcf Loading up the target reference genome.
INFO    2022-10-27 13:37:41 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.)
ERROR   2022-10-27 13:37:41 LiftoverVcf Encountered a contig, chr2 that is not part of the target reference.

I have seen multiple instances of this error online but I cannot find a single solution! I don't know if it is an issue with the chain file I am using being not exactly compatible to the New York Genome Centre release as it includes decoys and HLA, or whether it is a problem with the fact that chr21 in build 38 is just referred to as 21 in build 37. I tried to rename the header according to the hg19 reference, however, the latest version of bcftools reheader doesn't seem to support this function.