23andMe deletions

[mathiasbynens]

23andMe indicates deletions with D. Other groups use other standards.

genomejs/gql#4 (comment)
genomejs/gql#4 (comment)

[yocontra]

Found a bunch more info on the 23andme API docs

https://api.23andme.com/docs/reference/#genotypes

"For the user's profile, returns the base-pairs, like AA, for the given locations. The value can have Ds or Is for deletions and insertions (for example, DD or DI). It can be __ if the customer is not on a chip that calls that location, or hasn't yet unlocked their call since it corresponds to a sensitive report. It can be -- if the customer is on a chip that calls that location, but we could not determine it. To keep consistency with the /genomes endoint, which always returns two base pairs, hemizygous calls (such as on X-linked genes in males) will also return two base pairs."

Cases to cover correctly: --, DD, DI, __

For __ we should probably log an error that says the user needs to go click "unlock" or whatever on 23andme to get the data

[mathiasbynens]

Note that some users cannot unlock this data at all:

Your 23andMe kit was purchased on November 22, 2013 or later, granting you access to only ancestry information and uninterpreted raw data

[yocontra]

fixed in 1.1.2

[zhaofengli]

No call (-- in raw data) isn't the same as deletion. SNP-JSON perhaps should use ?? to indicate no-calls.

[yocontra]

@zhaofengli That makes sense, want to send a PR? I think https://github.com/genomejs/gql might need some tweaks for that.

Have you seen any docs on the 23andme csv format?