Introduction

Important

It is vital that the human genome build is the same for the GTF file, bed files, target file and the base file. Otherwise the coordinates of the SNPs can be wrong and PRSice will not be able to correctly assign the gene membership, leading to invalid results.

Command

  • --bed | -B

    Bed file containing the selected regions. Name of bed file will be used as the region identifier. WARNING: Bed file is 0-based

  • --feature

    Feature(s) to be included from the gtf file.

    Default: exon,CDS,gene,protein_coding

  • --gtf | -g

    GTF file containing gene boundaries. Required when --msigdb is used

    Tip

    Human Genome build GRCh38 can be downloaded from here.

  • --msigdb | -m

    MSigDB file containing the pathway information. Require the gtf file. The GMT file format used by MSigDB is a simple tab/space delimited text file where each line correspond to a single gene set following by Gene IDs: [Set A] [Gene 1] [Gene 2] ... [Set B] [Gene 1] [Gene 2] ...

    Tip

    Curated MSigDB files can be downloaded from here after registration in here

  • --set-perm

    The number of set base permutation to perform. This is only used for calculating the competitive p-value. 10,000 generally will be enough.

  • --snp-set

    Provide a SNP set file containing a single snp set. Name of SNP set file will be used as the region identifier. This file should contain only one column.

  • --snp-sets

    Provide a SNP set file containing multiple snp sets. Each row represent a single SNP set with the first column containing name of the SNP set.