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README.md

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Configuration

Different option can be change in the config/config.yaml file.

Output

With this set of options it's possible to change the output results folder and download resources path. All paths are relative to the running location. Either absolute path are accepted.

Results will be in the directory specified by output_dir, while quality control on genotype will be in the data_dir.

output_dir: "results"
data_dir: "data"

If some resources are already available from previous computation it's possible to reuse them specifing the cache_dir parameter.

# Cache directory for resources:
cache_dir: "/storage03/mfilosi/CKDgenPRS/prs_pipeline/resources"

Genotype QC

Parameters to use for quality controll process of the genotype. These are passed directly to plink for quality control with the relative options. See plink for the meaning of the options.

# Genotype QC parameters:
maf: 0.05
hwe: 1e-50
genorate: 0.1
mind: 0.1

LD reference

Definition of the reference panel for PRScs algorithm. Available options for population and data for LD panels are available here. Needed file are downloaded automatically based on the parameters defined here:

ld_reference:
  population: "eur"
  data: "1KG"

Algorithms

Activation of the algorithm to use for the analysis.

# PRS-method activation
prs_algorithms:
  ldpred2:
    activate: true
  lassosum2:
    activate: true
  prscs:
    activate: true
  sct:
    activate: true