Running FLAMES on DecodeME data

Alright I got POPs to run but unsure if some of the parameters I used are correct.

The setup:
  1. Cloned https://github.com/FinucaneLab/pops , then setup a virtual env using python 3.8 (it needs this for some of it's dependencies), installed requirements.txt in this env
  2. I then created a folder in this dir /pops/data
  3. I downloaded "pops_features_full_FUMA_compatible.tar.gz" unzipping into my pops/data dir
  4. I renamed the folder for ease of martins instructions "pops_features_full_FUMA_compatible" -> "pops_features_full"
  5. I then unzipped @forestglip MAGMA full results into my pops/data dir
  6. I then ran POPs using the following parameters as per instructions/parameters here
    1. python pops.py --gene_annot_path {USER DIR}/pops/data/pops_features_full/gene_annots.txt --feature_mat_prefix {USER DIR}/pops/data/pops_features_full/features_munged/pops_features --num_feature_chunks 116 --magma_prefix {USER DIR}\Documents\pops\data\magma --control_features {USER DIR}/pops/data/pops_features_full/control.features --out_prefix test
This created three files: test.coefs, test.marginals, test.preds

I think this worked, happy to upload the files if anyone can check?

Next the hard part, format credible sets.... I think I'll use FINEMAP: http://www.christianbenner.com/ need to spin up a linux distro real quick though
 
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