Question: detect human genome revision from RAW data (type 23andme) using SNP rsid
0
gravatar for zakrapovic
2.4 years ago by
zakrapovic0
zakrapovic0 wrote:

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 next-gen gwas genome • 819 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by zakrapovic0
0
gravatar for genomax
2.4 years ago by
genomax58k
United States
genomax58k wrote:

This should answer your question.

ADD COMMENTlink written 2.4 years ago by genomax58k

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?

ADD REPLYlink written 2.4 years ago by zakrapovic0

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.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax58k

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

ADD REPLYlink written 2.4 years ago by zakrapovic0
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