Where to get GERP_scores.final.sorted.txt.gz for VEP analysis

Question

[nikitavlassenko]

I need to run the pipeline:

https://github.com/macarthur-lab/hail-elasticsearch-pipelines/tree/master/luigi_pipeline

It has a VEP annotation step and the config file used is:

https://storage.googleapis.com/seqr-hail/vep/vep85-loftee-gcloud.json

In this file I need to set a bunch of paths to VEP files (I am running their pipeline locally) and I found all of them except the following one:

GERP_scores.final.sorted.txt.gz

I tried downloading it from:

https://personal.broadinstitute.org/konradk/loftee_data/GRCh37/

But it does not work. Could anyone explain how could I get the necessary data to run VEP for their pipeline VEP-annotation step (see line 126 of the file: https://github.com/macarthur-lab/hail-elasticsearch-pipelines/blob/d6e9dedbce929c04c294c54095663ba94a4de3f0/hail_scripts/v02/utils/hail_utils.py#L103) and where to get it?

The pipeline is built on top of Hail 0.2: https://hail.is/docs/0.2/methods/genetics.html?highlight=vep#hail.methods.vep

[GenoMax]

I tried downloading it from:

https://personal.broadinstitute.org/konradk/loftee_data/GRCh37/

But it does not work.

What does not work? I am able to click on the file link and get prompted to save the file. The file is 11G so I am not going to next step.

[nikitavlassenko]

The download is not working. If you go to the next step you will see that it is not going to be downloaded OR there are some weird Firewall rules on my job. I have not yet tried doing it outside from regular wifi.