Question: How to update a 23andme, vcf or plink bed file to hg38?
0
gravatar for Endre Bakken Stovner
4.6 years ago by
Norway
Endre Bakken Stovner880 wrote:
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 • 2.1k views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Endre Bakken Stovner880

how does it look like ?

ADD REPLYlink written 4.6 years ago by Pierre Lindenbaum119k
Almost like a bed file. Will post tomorrow, using phone now.
ADD REPLYlink written 4.6 years ago by Endre Bakken Stovner880
0
gravatar for Pierre Lindenbaum
4.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

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

ADD COMMENTlink written 4.6 years ago by Pierre Lindenbaum119k
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?)
ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Endre Bakken Stovner880

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

ADD REPLYlink written 18 months ago by 141341254653464453.4k

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

ADD REPLYlink written 3 months ago by OK_0

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 .

ADD REPLYlink written 4.6 years ago by chrchang5234.9k
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