running MetaXcan with Blueprint eQTL summary statistics

[IoannaTachmazidou]

Dear MetaXcan authors,

I would like to run MetaXcan with Blueprint. I have downloaded Blueprint genome-wide eQTL summary statistics, but I don't have the raw data. I thought I could still use MetaXcan, but now having gone through the example for creating the input files and databases (necessarily through PrediXcan), I don't think I can anymore. Can you please confirm if one can run MetaXcan having only genome-wide eQTL summary statistics? Many thanks.

Best,
Ioanna

[rbonazzola]

Hello Ioanna,

You are correct: currently there is no support for eQTL summary statistics as input for PrediXcan or MetaXcan. However, we are working on a tool that will allow you to obtain prediction models for gene expression in the format accepted by both programs (SQLite databases), from summary eQTL data (precisely what you are needing here). I happen to be working on this project at the moment, and hope to have some working code within a few weeks. If you are interested, I can contact you then, so you can generate models based on Blueprint eQTL summary statistics.

Best,
Rodrigo

[IoannaTachmazidou]

Excellent, I am very much interested, please contact me once you are ready. Many thanks!

[IoannaTach]

Dear Rodrigo,

I was wondering if there was any progress in your work on extending MetaXcan/PrediXcan to work with eQTL summary statistics? i am very keen to use it very soon for a manuscript I am preparing. Many thanks.

Best,
Ioanna

[rbonazzola]

Dear Ioanna,

Yes, we'll have a first version of the tool released as a web application, really soon. You'll be able to upload your eQTL summary statistics files and get the prediction models and the covariance matrices (needed for MetaXcan) as output. We expect to have this first version within one week, hopefully. Thanks for your interest!

Best,
Rodrigo

[IoannaTach]

Excellent, thank you.

[IoannaTach]

Hi Rodrigo,

Do you have any updates please? :-)

Ioanna

[rbonazzola]

Hi Ioanna,

I am sorry for not reaching back earlier, but unfortunately the release of the web app got delayed, however I have some scripts in a public GitHub repository that you can use to do the conversion (this). Since they are not documented yet, I just sent you an e-mail so I can help you use them for your particular data.

Best,
Rodrigo

[Heroico]

Closing due to inactivity, assuming it fixed.