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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:

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