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This page contains all command available in BridgePRS.

Tips

When constructing new parameters, we follow the following rule: if the command has effect on any file that is not the target, it will have a prefix of the file name. For example, --base-info applies INFO score filtering on the base file, --ld-info perform INFO score filtering on the LD reference file and --info applies the INFO score filtering on the target file.

Input Population Files/Arguments

  • --sumstats_prefix Path to sumstats data

  • --sumstats_suffix Sumstats Suffix

  • --phenotype_files phenotype test and validation data

  • --pop_config(s) population configuration file(s)

  • --pop or --pops population names (AFR, EUR, etc)

  • --snp_file List of QCed SNP ids

System Level Toggles/Arguments

  • --cores By default bridgePRS is parralelized across (n-1) cores

  • -o Output folder for BridgePRS

  • --platform Force platform (Linux or MacOS)

  • --verbose Toggle Verbose Mode On

  • --noPlots Skip Post-Pipeline Analysis (Plotting)

  • --restart Repeat previously completed steps

Parameter Arguments

  • --fst fst between populations analysed, e.g. 0.15 for Africans v Europeans and 0.11 for East Asians v Europeans

  • --strand_check Logical to check whether summary statistics and reference data input files are on the same strand. If true/1 only unambiguous SNPs are used in analyses. If false/0 all variants with matching alleles between studies are used. With both options effect and reference alleles are checked and flipped where necessary. If a matching pair of alleles is not found variants are removed (default 0)

  • --max_clump_size Maximum number SNPs allowed in a clump. Very large clumps, eg more than 1,000 variants, can occur in regions of high LD such as the HLA region when using imputed data and considerably slow the algorithm. Must be used in conjunction with --thinned_snplist, see below

  • --thinned_snplist Thinned snp list to use for clumps that exceed --max_clump_size, list of HapMap variants would be suitable

Internal File Arguments

  • --model_file model result generated from the build-model subprogram

  • --clump_prefix prefix for files generated by clump step

  • --beta_prefix prefix for files generated by beta step

  • --predict_prefix prefix for files generated by predict step

  • --result_file prs result files

File Column Names

Phenotype Files

  • --phenotype Phenotype File Field: phenotype
  • --covariates Phenotype File Field: comma separated list of covariates

Sumstats Files

  • --ssf-snpid Sumstats field: snp ID

  • --ssf-ref Sumstats Field: reference allele

  • --ssf-alt Sumstats Field: alt allele

  • --ssf-maf Sumstats Field: MAF

  • --ssf-beta Sumstats Field: linear regression effect or log odds

  • --ssf-se Sumstats field: standard error

  • --ssf-p Sumstats field: P-value

  • --ssf-n Sumstats Field: Sample Size