Can I run these scripts locally or on an HPC-server?

[yangyxt]

First of all, thank you for making such a great metric. It really helps.

I see in your tutorial, you recommend to run this script on a publicly available cloud server. I wonder whether is this cloud server openly and freely accessible to everyone online? Can I just run this locally?

I tried to run this script locally, but all the data are on google cloud storage and I need to use gsutil to access them. Most of the data is available, but when I tried to access vep_config(the json file) I got an error: Bucket is requester pays bucket but no user project provided.

[yangyxt]

Also, can this tutorial be applied to indels? Instead of SNVs?

[berylc]

Hi! So sorry I'm just seeing this - need to update my notification settings.

To answer your second question first, yes the method can definitely be applied to indels as well as SNVs.

To solve a requestor bucket pays problem, you need to specify a google project with -u. I am personally unsure how to access google bucket storage without an account of your own, but can ask in my team if useful.

Before that though, I urge you to consider using the pre-computed pext metrics on every SNV in the genome. This is for GTEx samples.

Let me know if this is related to calculating pext on an internal transcript expression dataset. Our method relies on Hail (which for the record can be run on AWS as well). But happy to figure out a way to get your calculations performed as well.