• --A1

Column header containing the effective allele. There isn't any standardized label for the effective allele, therefore extra care must be taken to ensure the correct label is provided, otherwise, the effect will be flipped.

• --A2

• --base | -b

Base (i.e. GWAS) association file. This is a whitespace delimited file containing association results for SNPs on the base phenotype. This file can be gzipped (must have the .gz suffix). For PRSice to run, the base file must contain the effective allele (--A1), effect size estimates (--stat), p-value for association (--pvalue), and the SNP ID (--snp).

• --beta

This flag is used to indicate if the test statistic is in the form of BETA. When not set, PRSice assume the statistic is in the form of Odd Ratios, perform natural log transformation on the test statistic.

• --bp

Column header containing the coordinate of SNPs. When provided, the coordinate of the SNPs will be scrutinized between the base and target file. SNPs with mismatched coordinate will be excluded.

• --chr

Column header containing the chromosome information. When provided, the chromosome information of the SNPs will be scrutinized between the base and target file. SNPs with mismatched chromosome information will be automatically excluded.

• --index

If set, assume the base columns are INDEX instead of the name of the corresponding columns. Index should be 0-based (start counting from 0)

• --info-base

Base INFO score filtering. Format should be <Column name>,<Threshold>. SNPs with info score less than <Threshold> will be ignored. It is useful to perform INFO score filtering to remove SNPs with low imputation confidence score. By default, PRSice will search for the INFO column in your base file and perform info score filtering with threshold of 0.9. You can disable this behaviour by using --no-default

• --maf-base Base minor allele frequency (MAF) filtering. Format should be <Column name>,<Threshold>. SNPs with MAF less than <Threshold> will be ignored. Additional column can be provided (e.g. different filtering threshold for case and control), using the following format: <Column name>,<Threshold>:<Column name>,<Threshold>

• --no-default Remove all default options. If set, PRSice will not set any defaults.

• --pvalue | -p

Column header containing the p-value. The p-value information must be provided

• --se

Column header containing the standard error. Currently, this serves no purpose.

• --snp

Column header containing the SNP ID. This is required to allow SNP matching between the base and target file.

Note

While it is possible to implement a feature to allow SNP matching purely based on the chromosome number and coordinate of a variant, the possibiliy of flipping and multi-allelic input complicates the matter. Therefore this feature will not be implemented until an elegant solution can be provided.

• --stat

Column header containing the summary statistic. If --beta is set, default as BETA. Otherwise, try and search for OR or BETA from the header of the base file. If both OR and BETA is presented in the header, PRSice will terminate.