• --clump-kb The distance for clumping in kb. For example, if --clump-kb 250 is provided, PRSice will clump any SNPs that is within 250kb to both end of the index SNP (therefore a 500kb window with the index SNP at the center). Default: 250

• --clump-r2

The r2 threshold for clumping. Default: 0.1

• --clump-p

The p-value threshold use for clumping. Default: 1.

• --ld | -L

LD reference file. Use for estimation of LD during clumping. If not provided, will use the post-filtered target genotype for LD calculation. Support multiple chromosome input. Please see --target for more information. When the target sample is small (e.g. < 500) and external panel of the same population is available (e.g. 1000 genome), an external reference panel might be used to improve the LD estimation for clumping.

• --ld-geno

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

• --ld-info

Filter SNPs based on info score. Only used for imputed LD reference. 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

• --ld-hard-thres

Hard threshold for dosage data. Any call less than this will be treated as missing.Default: 0.9

• --ld-keep

File containing the sample(s) to be extracted from the LD reference 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 --ld-remove. No effect if --ld was not provided - --ld-list

File containing prefix of multiple LD reference files. Similar to --ld but allow more flexibility. Do not support external fam file at the moment

• --ld-maf

Filter SNPs based on minor allele frequency (MAF)

Note

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

• --ld-remove

File containing the sample(s) to be removed from the LD reference 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 --ld-keep

• --ld-type

File type of the LD file. Support bed (binary plink) and bgen format. Default: bed\n"

• --no-clump

When set, PRSice will not perform clumping. This is useful a pre-clumped list of SNPs is available.

• --pearson

Use Pearson Correlation instead of maximum likelihood haplotype frequency estimates for LD calculation

• --proxy

Proxy threshold for index SNP to be considered as part of the region represented by the clumped SNP(s). e.g. --proxy 0.8 means the index SNP will represent region of any clumped SNP(s) that has r2=0.8 even if the index SNP does not physically locate within the region