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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

  • --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 value

  • --max_clump_size Max Size for Clumping

  • --thinned_snplist Thinned snp list for large clumps

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: covariates

Sumstats Files

  • --ssf-alt Sumstats Field: alt allele

  • --ssf-beta Sumstats Field: beta

  • --ssf-maf Sumstats Field: MAF

  • --ssf-p Sumstats field: P-value

  • --ssf-ref Sumstats Field: reference allele

  • --ssf-se Sumstats field: standard error

  • --ssf-snpid Sumstats field: snpID

  • --ssf-n Sumstats Field: Sample Size

  • --sumstat_prefix path to sumstats file prefixes

  • --sumstats_suffix Sumstats Suffix