23andme raw data analysis


#1

Has anyone used HAIL to analyze raw data from 23andme for further insights?

If so, can you describe high level steps, and any interesting results/analysis to try.


#2

Can you provide a bit more information about what you’re looking to do? The help we’re qualified to offer is primarily technical, not scientific.


#3

at the most basic level - can hail parse raw data from 23andme - but i can see how this might be not be super useful for an armchair enthusiast like myself, if i don’t know what analysis i am looking to do in the first place!


#4

What file format? Hail can parse PLINK files, which is a standard gneotype chip format.


#5

Based on the description provided by 23andme, you could load your data as a four column KeyTable using HailContext.import_table. Now you have an RSID, Chromsome, Position, and genotype table. But you haven’t achieved much more than loading your data into a SQL-like system.

There’s not much you can do with this data. Hail really shines when you have a large dataset, particularly of many sequenced genomes.

A book like Exploring the Personal Genome might help you understand what questions you want to ask.


#6

for posterity - in case some newbie stumbles on this as well - these site is super useful -
https://www.promethease.com


#7

I am late to the party but Xcode Life is also a great website to try: https://www.xcode.life


#8

gnomAD is also a great resource for exploring genomic variation, either through the website or with Hail (for example, you could annotate your genome with gnomAD’s info and then filter to find your rare, loss-of-function variants):
http://gnomad.broadinstitute.org/