Description
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?