Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Sex chromosome phewas variant queries fail #9

Open
thirtysix opened this issue Oct 31, 2022 · 0 comments
Open

Sex chromosome phewas variant queries fail #9

thirtysix opened this issue Oct 31, 2022 · 0 comments

Comments

@thirtysix
Copy link

I have recently been trying to use the OpenGWAS service (lovely work by the way) to look at a gene on the X chromsome. I have a script to use the API, which has worked well with other regions now and in the past, but I am realizing it seems to be failing on sex chromosome queries.

Here is an example curl:
curl -X POST 'http://gwas-api.mrcieu.ac.uk/phewas?variant=X:15704453-15809034&pval=0.001' -H 'accept: application/json' -H 'X-Api-Token: null'
Same query, generated from the endpoint documentation:
http://gwas-api.mrcieu.ac.uk/phewas/X%3A15688830-15788411/0.001

I have tested several 1 million base pair stretches on several different non-sex chromosomes (locs 10-11 million) and they all seem to work, but the same query on both X and Y chromosomes fail instantly.

As another test, I found a variant on Gtexportal.org in this region (rs5936049) and then queried it on OpenGWAS http://gwas-api.mrcieu.ac.uk/phewas/rs5936049/0.001. The query succeeds and in the results the chromosome is listed as "X".

So, either I am setting up the queries wrong, I couldn't find any documentation on sex chromosomes specifically, or there might be some issue with how the API handles non-numeric chromosome queries. Perhaps it's coercing the input str to numeric and failing? I also tried using 23/24 as the chromosome id, but that didn't work either.

Any thoughts?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant