Introduction

raimondsre/polygenictest is a bioinformatics pipeline that calculates individual polygenic score percentile in the population.

1. Read genome file
2. Apply quality control
3. Impute missing genotypes
4. Calculate polygenic risk score

Usage

Note

If you are new to Nextflow, please refer to this page.

Now, you can run the pipeline using:

nextflow run raimondsre/polygenictest \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters;

Credits

raimondsre/polygenictest was originally written by raimondsre.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.