Isn't this swapped?
[in https://github.com/freeseek/score/blob/master/liftover.c, lines 837-842]
liftover_target_reference x src_ref_fname
if (src_ref_fname)
bcf_hdr_printf(out, "##liftover_target_reference=%s",
strrchr(src_ref_fname, '/') ? strrchr(src_ref_fname, '/') + 1 : src_ref_fname);
liftover_query_reference x dst_ref_fname
if (dst_ref_fname)
bcf_hdr_printf(out, "##liftover_query_reference=%s",
strrchr(dst_ref_fname, '/') ? strrchr(dst_ref_fname, '/') + 1 : dst_ref_fname);
if it is intended to be that way, please ignore this issue