How to update a 23andme, vcf or plink bed file to hg38?

Question

[Endre Bakken Stovner]

Hos do I upgrade a 23andme file to the latest genome versjon, hg38? That it isn't possible to do reliably is also an answer, but hopefully it is simple. Edit: is there a tool that changes genotypes too, not just position? Or is a woman with A/T in snp x certain to have the same alleles after the snp upgrade? Since plink2 can convert the 23 format, I'll accept answers for VCF and plink bed too.

[Pierre Lindenbaum]

how does it look like ?

[Endre Bakken Stovner]

Almost like a bed file. Will post tomorrow, using phone now.

Answer 1

[Pierre Lindenbaum]

It's a bed file ? Use liftover https://genome.ucsc.edu/cgi-bin/hgLiftOver

[Endre Bakken Stovner]

Thanks, but how do you know which alleles a person has after the upgrade? That tool just converts genome positions, it does not do anything to the genotype afaicr (if a SNP has genotype AA in hg36, is it guaranteed to be the same in hg38?)

[14134125465346445]

Has anybody produced a bed file for the 23andme rsIDs on hg38?

[OK_]

Yes, if by bed you mean plink-style bed file.

[chrchang523]

plink bed is not the same thing as UCSC bed. However, there are scripts for bridging the difference: see e.g. http://genome.sph.umich.edu/wiki/LiftOver