# Introduction¶

Base (i.e. GWAS) data must be provided as a whitespace delimited file containing association analysis results for SNPs on the base phenotype. PRSice has no problem reading in a gzipped base file.

If you are using output from PLINK, then please make sure there is a column for the effect allele (A1) and specify it with --A1 option. On the other hand, if you are using another form of output, then you can provide the column headers using the --chr, --A1, --A2, --stat, --snp, --bp, --se, --pvalue options

Important

For PRSice to run, the base file must contain the effect allele (--A1), effect size estimates (--stat), p-value for association (--pvalue), and the SNP id (--snp).

If the input file does not contain a column header, then you can specify the column using their index (start counting from 0) with the --index flag.

e.g. if the first column of the file contains the p-value information, you can use: --pvalue 0 --index

Below is an example input file:

SNP CHR BP A1 A2 OR SE P
rs3094315 1 752566 A G 0.9912 0.0229 0.7009
rs3131972 1 752721 A G 1.007 0.0228 0.769
rs3131971 1 752894 T C 1.003 0.0232 0.8962

and the parameters can either be

--snp SNP --chr CHR --bp BP --A1 A1 --A2 A2 --stat OR --se SE --pvalue P

or

--snp 0 --chr 1 --bp 2 --A1 3 --A2 4 --stat 5 --se 6 --pvalue 7 --index

Strand flips are automatically detected and accounted for

If an imputation info score or the minor allele frequencies (MAF) are also included in the file, you can use --info-base <Info Name>,<Info Threshold> and --maf-base <MAF Name>,<MAF Threshold> to filter SNPs based on their INFO score and MAF respectively.

For binary trait base file, you can also filter the MAF according the the case and control separately using

--maf-base <MAF Name for Control>,<MAF Threshold for Control>:<MAF Name for Case>,<MAF Threshold for Case>


By default, PRSice will look for the following column names automatically from your base file header if --index was not provided:

CHR, BP, A1, A2, SNP, P, INFO, SE (case sensitive) and OR / BETA (case insensitive)

If you don't want the specific column to be included e.g. You don't want to perform info score filtering but your file contains an INFO column, you can use --no-default to disable all the defaults of PRSice. PRSice will ignore any columns that were not found in your file (e.g. If you specified --A2 B but none of your column header is B, then PRSice will treat it as if no A2 information is presented)

# Commands¶

• --A1

Column header containing the effective allele. As there is not a standardized name, please make sure you have provided the correct column. Otherwise, the effect will be flipped.

• --A2

Column header containing non-effective allele. As there is not a standardized name, please make sure you have provided the correct column. Otherwise, the effect will be flipped.

• --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. For PRSice to run, the base file must contain the effect 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. If set, test statistic is assume to be in the form of BETA

• --bp

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

• --chr

Column header containing the chromosome information. When this is 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. An additional column can also be added (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 and you will have to ensure all required columns are provided. (--snp, --stat, --A1, --pvalue)

• --pvalue | -p

Column header containing the p-value. The p-value information is required for clumping and this information must be provided under all circumstances.

• --se

Column header containing the standard error. Currently we do not use the standard error in any of the analysis. Thus this column is not required.

• --snp

Column header containing the SNP ID. This is required such that we can match SNPs between the base and target file.

• --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. The summary statistic is required for the construction of PRS.