use FUMA GWAS programmatically

[alessandr...@gmail.com]

Hi!
I have small regions coming from different GWAS datasets to be analyzed. I'm only interested in these regions, since they pass several criteria (e.g.: association p-value threshold < threshold, epigenetic features ...). I'm afraid it would take too long to load all the GWAS subsets. Is there a way to use FUMA GWAS programmatically (e.g.: API)? Please let me know. Thanks!

[Kyoko Watanabe]

Hi,

Thank you for your comments.

I understand that entire process of FUMA actually takes long if you are only interested in a sew locus.

Unfortunately, we currently do not have solid plan of API due to large amount of pre-procesed data that FUMA requires, however, since this is not the first time to get question about API, we will consider developing API.

As a temporal solution, by uploading a subset of SNPs that you want to annotate not the full GWAS results, this can shorten the process time but the MAGMA results won't be informative in this case.

Best,

Kyoko

[amai...@gmail.com]

Hi!
I just wanted to note that I'd also love in being able to use FUMA GWAS programatically - to upload several GWASes in a consistent manner.
Thanks for this great tool! :)
amaia

[Kyoko Watanabe]

Hi Amaia,

Thank you for your comment.

As we are getting more and more request, we are considering developing API.

I can not promise when it's going to be but I will do my best.

Best,

Kyoko

[Ram]

Hello Kyoko and all the team at FUMA-GWAS:

Thank you very much for this tool!

I would also like to echo my interest in an API/programatic access version. I work with multiple sets of genes that I have to manually upload and set settings for in the GENE2FUNC module, then manually download to my computer. Having a way to connect to FUMA-GWAS -preferrably through the terminal- and automatically going through the steps with my gene lists would save me hours of work :-) 

Best,
Ram