VCF file transfer to a better genome

Question

[Nilo]

Hi everyone, I had an old, contig, genome and a corresponding .vcf file with many parental lines mapped against that old genome.

I know have a new genome and want to transfer the variants to this new genome and create a new .vcf file.

Anyone an idea on if this is possible and how to do so?

Thanks in advance!

[barslmn]

I would do the analysis from the start. Otherwise you need to create a chain file between the genomes and do a liftover.

Answer 1

[colindaven]

Definitely re-do the analysis from the start if your new genome is of better quality. Check the N50 of both of these and the BUSCO values if in doubt. And/or map known proteins to both with miniprot and check recovery rates etc.

You'll never get the same accuracy by using an old genome which is only say 80% of the accuracy of the new genome and trying to take the old, incorrect results and map them over. If you or your predecessor used a pipeline system like Nextflow then it should be repeatable - if not, it might be time to start learning one.