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How to update a 23andme, vcf or plink bed file to hg38?
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.
23andme
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updated by Ram Ram • written by Endre Bakken Stovner Endre Bakken Stovner
Almost like a bed file. Will post tomorrow, using phone now.
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written by Endre Bakken Stovner Endre Bakken Stovner

1 answer

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

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written by Pierre Lindenbaum Pierre Lindenbaum
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?)
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written by Endre Bakken Stovner Endre Bakken Stovner

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

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written by 14134125465346445 14134125465346445

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

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written by OK_ • OK_

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