# Basic Commands¶

• --binary-target

Indicate whether the target phenotype is binary or not. Either T or F should be provided where T represent a binary phenotype. For multiple phenotypes, the input should be separated by comma without space.

Default: F if --beta is set and T otherwise

• --geno

Filter SNPs based on gentype missingness. Must be a value between 0.0 and 1.0.

• --info Filter SNPs based on info score. Only used for imputed target data. The INFO score is calculated as the MaCH imputation r-squared value, represented by the following pseudo code:

    m=Mean of expected genotype
v=variance of expected genotype
p=m/2
p_a = 2p(1-p)
INFO = v/p_a

• --keep

File containing the sample(s) to be extracted from the target file. First column should be FID and the second column should be IID. If --ignore-fid is set, first column should be IID Mutually exclusive from --remove

• --maf

Filter SNPs based on minor allele frequency (MAF)

Note

When perform MAF filtering on dosage data, the MAF is calculated using the hard-coded genotype

• --nonfounders

By default, PRSice will exclude all non-founders from the analysis. When this flag is set, non-founders will be included in the regression model but will still be excluded from LD estimation.

• --pheno-col

Headers of phenotypes to be included from the phenotype file. When multiple phenotypes are provided, the phenotype name will be used as part of the file output prefix

• --pheno-file | -f

Tab or space delimited phenotype file containing the phenotype(s). First column must be FID of the samples and the second column must be IID of the samples. When --ignore-fid is set, first column must be the IID of the samples. Must contain a header if --pheno-col is specified

• --prevalence | -k

Prevalence of all binary trait. If provided, PRSice will adjust the ascertainment bias of the R2.

Note

When multiple binary trait is found, prevalence information must be provided for all of them (Either adjust all binary traits, or don't adjust at all). For example, if there are 3 traits A, B and C, where A and C are binary traits with population prevalence of 0.1 and 0.2 respectively. The correct input should be --binary-target T,F,T --prevalence 0.1,0.2

• --remove

File containing the sample(s) to be removed from the target file. First column should be FID and the second column should be IID. If --ignore-fid is set, first column should be IID Mutually exclusive from --keep

• --target | -t

Target genotype file. Currently support both BGEN and binary PLINK format. For multiple chromosome input, simply substitute the chromosome number with #. PRSice will automatically replace # with 1-22. A separate fam/sample file can be specified by --target <prefix>,<fam/sample file>

• --type

File type of the target file. Support bed (binary plink) and bgen format. Default: bed

# Dosage Related Commands¶

• --allow-inter

Allow the generate of intermediate file. This will speed up PRSice when using dosage data as clumping reference and for hard coding PRS calculation

• --hard-thres

Hard threshold for the dosage data. SNPs with be coded as the genotype with probability higher than the threshold specified here. If no such genotype is presented, the SNP will be treated as missing.

Note

If dosage data is used as a LD reference, it will always be hard coded to calculate the LD

Default: 0.9

• --hard

When set, will use hard thresholding instead of dosage for PRS construction. Default is to use dosage.