PRSice-nf

Pipeline to compute polygenic risk scores

Input

Type --help to get the full list of options. All parameters are prefixed with a double-dash like in --help.

Name	Example value	Description
bgen_list	bgen_list.txt	Txt file containing the list of bgen files to consider (one file per chromosome)
base_file	base.txt	file containing association analysis results for SNPs on the base phenotype
pheno_file	pheno.txt	phenotype file: the first two column of the phenotype file should be the FID and the IID and the rest of the columns the phenotypes

For more details on the files content, see PRSice2 documentation

Parameters

• Mandatory

Name	Example value	Description
bgenix	bgenix	path to bgenix executable
PRSice_path	path_PRSice	path to PRSice scripts

• Optional

Name	Example value	Description
a1_col	4	Column number associated with the effect allele (Default value is 4)
a2_col	5	Column number associated with the reference allele (Default value is 5)
qual_val	0.3	Quality threshold. Any SNPs with a value bellow this threshold will be excluded. (Default value is 0)
pval_thr	0.0001,0.1,1	pvalue threshold to consider to select SNPs to include in the PRS

To install:

• bgen
• PRSice2

Nextflow command line

nextflow run  IARCbioinfo/PRSice-nf \
  --base_file base.txt \
  --pheno_file /data/gep/MR_Signatures/work/gabriela/GIT_Rstudio_project/results/PRSice_res/TCGA_samples.txt  --pval_thr 1 \
  --output_name ${trait} --output_folder /data/gcs/prs-computation/work/gabriela/PRS_R_project/results/PRSice_res/${trait}/ \
  --bgenix path_to_bgenix --PRSice_path path_to_PRSice \
  --bgen_list bgen_list.txt \
  --bgen_snps_perCHR /data/gep/MR_Signatures/work/gabriela/GIT_Rstudio_project/results/PRSice_res/TCGA_bgen_SNPs/ --qual_val 0.3