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.


  • --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


    Human Genome build GRCh38 can be downloaded from here.

  • --msigdb | -m

    MSIGDB file containing the pathway information. Require the gtf file. The MSigDB file format 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] ...


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