23andme files uses GRCh37 or GRCh38 ?
1
0
Entering edit mode
6.3 years ago
ahm3dhany ▴ 10

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

23andme orientation reference genome genome • 2.2k views
ADD COMMENT
5
Entering edit mode
6.3 years ago
Denise CS ★ 5.2k

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

ADD COMMENT
1
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
2
Entering edit mode

Please ask this as a new question.

ADD REPLY

Login before adding your answer.

Traffic: 723 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6