I got a quite tricky task to liftover SNPs from NCBI assembly to ENSEMBL assembly. The assemblies are different i.e. the chromosome lengths and the chromosome names. Furthermore ENSEMBL assembly is not present at NCBI and vice-versa so the using tools like NCBI Genome Remapping Service or the ENSEMBL Assembly Converter will not help.
I guess the tool which picks the VCF and/or BED file plus the corresponding fasta file for the one assembly and fasta file of the assembly that I want to liftover my SNPs and outputs the file of SNP matches already exist. If so, please, suggest or recommend some other ways to do this. All I need is just the updated positions of SNPs, annotation related stuff is not of interest.
It is Brassica napus genome and unfortunately, the specialised Brassica genome database does not have a feature related to SNP liftover between the ZS11 and Darmor-bzh assemblies.