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detect human genome revision from RAW data (type 23andme) using SNP rsid

I have RAW data for different sample, coming mostly from 23andme.
Some are without header.

How can I find out which human genome revision reference has been used to annotate them?

The next step will be to lift them all to the same revision.

Thanks

snp snp genome next-gen gwas
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written by zakrapovic • zakrapovic

2 answers

This should answer your question.

• 1 views • link
written by GenoMax GenoMax

First thanks for answering,

The problem is that I do not only have 23andme data, some are in similar format but come from other direct-to-consumer genetic testing. Even if we only consider 23andme, some data from them are 5 years old and were based on build 36.

So the question is still open, for example based on a big set of rsid, is it possible to determine the build?

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written by zakrapovic • zakrapovic

Being able to determine genome build based on rsid that may be a tall order. Someone more knowledgeable may have a better answer later.

Update: An accepted answer for this thread (Question about dbSNP rs #s ) indicates that rsID's will stay the same from genome build to genome build. If that is correct then the answer for your question will be a no, you can't determined genome build from rsID.

• 1 views • link
written by GenoMax GenoMax

No but the couple RSID + position could do it :).
I will update and post answer when I will be done with it.

• 1 views • link
written by zakrapovic • zakrapovic

First thanks for answering,

The problem is that I do not only have 23andme data, some are in similar format but come from other direct-to-consumer genetic testing.
Even if we only consider 23andme, some data from them are 5 years old and were based on build 36.

So the question is still open, for example based on a big set of rsid, is it possible to determine the build?

• 0 views • link
written by zakrapovic • zakrapovic

Please use the ADD COMMENT button on my post to add this information there. SUBMIT ANSWER should only be used for new answers for the original question.

As for being able to determine genome build based on rsid that may be a tall order. Someone more knowledgeable may have a better answer later. This is an old post but possibly still applicable: Repeated Rsids In Dbsnp?

• 1 views • link
written by GenoMax GenoMax

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