You Shouldn't Be Using Raw 23andMe Data for Analysis
There are a growing number of services offering to analyze your raw data from genetic testing companies like 23andMe. These sites claim to give you additional insight into your genome beyond the ancestry and health data officially validated by the companies you purchased your testing from.
Although these testing companies provide ways to export your raw data, many people don't seem to realize that it's a mixture of validated and unvalidated genetic code and therefore could be misleading if assumed to be totally accurate.
A growing number of genetic services
There are a growing number of free and paid services that claim to provide deeper insight into your raw genetic data. This is appealing because sites like 23andMe are careful about the claims they make and the reports they provide to consumers are limited.
Third-party services have fewer restrictions. They include popular free sites like Promethease, which matches your data to open-source genetic research, and sites like Xcode.life, which claims to analyze 600 different traits for a fee.
Your raw data is not validated for accuracy
23andMe provides a warning when you request your raw genotype data:
Only a subset of markers have been individually validated for accuracy. As such, the data ... is suitable only for research, educational, and informational use and not for medical, diagnostic or other use.
Essentially what they're is saying is that only select data (which are analyzed in the health reports 23andMe provides) have been individually validated for accuracy. Any additional genetic data, although collected via their laboratory testing, cannot be relied on for interpretation of medical conditions.
One study that analyzed direct-to-consumer genetic services like 23andMe concluded that "40% of variants in a variety of genes reported were false positives". As mentioned above, this is likely because services like 23andMe only validate certain portions of the DNA that they plan to use for their own health reports.
Although the study doesn't name any companies directly, it does indicate that the type of services considered in the study could include Family Tree DNA, My Heritage, 23andMe, and Ancestry.com.
Take caution when uploading your raw genetic data to any third-party services outside of your 23andMe account. These include services that offer to provide a health interpretation of your raw data in addition to public genealogy websites.
Raw genetic data, unless validated by professional testing, should not be used for medical purposes. Reports or analysis that any third-party services make may not be accurate and should be viewed with skepticism.