Question: 23andme files uses GRCh37 or GRCh38 ?
0
gravatar for ahm3dhany
19 months ago by
ahm3dhany10
ahm3dhany10 wrote:

Does anyone know if 23andme switched to GRCh38 or they are still using GRCh37?

ADD COMMENTlink modified 19 months ago by Devon Ryan74k • written 19 months ago by ahm3dhany10
5
gravatar for Denise - Open Targets
19 months ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.1k wrote:

According to Which reference genome does 23andMe use?, it's GRCh37.

ADD COMMENTlink written 19 months ago by Denise - Open Targets4.1k
1

I can confirm this is currently the case by cross-referencing the coordinates in my raw 23andme data with dbSNP. (e.g. rs13096 is at coordinate 25359841, not 25206907)

ADD REPLYlink written 19 months ago by Keith Callenberg870

Another question to clear up the confusion.. I am comparing the genotypes of rsIDs from the 23andme files versus the genotypes from snpedia.

23andme file for individual X:

enter image description here

on snpedia (for rs4988235):

enter image description here

on snpedia (for rs9939609):

enter image description here

after making some comparisons the results (i.e. the results i deduced):

enter image description here

if you noticed, in case of rs4988235 i flipped (i.e. converted) the genotype AA to TT because SNPedia shows that the orientation is minus, whereas i didn't flip the genotype for the rs9939609 because the orientation is plus.

So my question is, am I doing it the right way? I apologize if my question is naive, my background is in computer science not genomics.

ADD REPLYlink modified 19 months ago • written 19 months ago by ahm3dhany10
2

Please ask this as a new question.

ADD REPLYlink written 19 months ago by Ram13k
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