emkoch / smilenfer

Inference of simple selection models from the distribution of genetic associations.

Genetic association data are broadly consistent with stabilizing selection shaping human common diseases and traits

Project components

gwas_processing

Code for downloading and processing GWAS summary statistics.

results

Processed GWAS summary statistics, model fits, simulation output, and scripts for generating figures.

smilenfer

Main code used for analyses, simulations, and plotting. This is organized as a python package and which can be installed by first creating a conda environment with the necessary dependencies conda env create -f smilenfer.yml. After activating the environment run install.sh.

snakemake

Snakemake piplines used for model fits and simulations. After installing the pacakge, this is how model fits are actually performed.

More information on requirements and runtime can be found in example_trait/example_trait_analysis.sh

smilenfer's Issues

Running quantitative traits

Hi,

I want to run smilenfer for some quantitative traits. I have been able to reproduce the test trait (bc), but am wondering what I should change in the analysis pipeline to run quantitative traits. I have noticed that I should at least change some things in the test_run.yml file, but am not sure which parts to change and which not. Also, should I change anything else somewhere?

Thanks a lot!
Anaïs

Changing threshold

Hi!
Another question. I want to run the software on another threshold. I already changed the ash and clump scripts. But when I change the theshold in the .yml file (p_threshes: ["5e-08"] and p_cutoffs: ["5e-08"]) to "1e-04" I get the following error message:

Error in rule llhood_calc:
jobid: 0
input: ../../results/data/clumped_ash/clumped.p0001_ash.SCZ.tsv, output/WF_pile.pkl
output: scratch/SCZ_orig_0.0001_nonplei.pkl, scratch/SCZ_orig_0.0001_plei.pkl

RuleException:
KeyError in file /gpfs/home2/anais1/evo_psych/smiles/smilenfer/snakemake/Snakefile_trait_fits_simple, line 304:
'0.0001'
File "/gpfs/home2/anais1/evo_psych/smiles/smilenfer/snakemake/Snakefile_trait_fits_simple", line 304, in __rule_llhood_calc
File "/home/anais1/.conda/envs/smilenfer-4/lib/python3.9/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

How should I proceed?