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