| OPTION |
FUNCTION |
| --autoQC |
Quality control (QC) including call rate and gender checking |
| --bim |
Specify .bim file as alternative input |
| --build |
Reconstruct pedigrees using information from SNP data |
| --bysample |
Sample-level QC |
| --bySNP |
SNP-level QC |
| --callrateM |
Specify SNP-level call rate for QC |
| --callrateN |
Specify sample-level call rate for QC |
| --cluster |
Cluster individuals into families according to inferred relatedness |
| --covariate |
Specify covariate names to be adjusted in association analysis |
| --cpus |
Specify number of CPU cores for parallel computing |
| --degree |
Specify degree of relatedness for all relatives to be inferred |
| --duplicate |
Identify duplicate pairs (including MZ twins) using autosome SNP data |
| --fam |
Specify .fam file as alternative input |
| --homog |
Infer relatedness assuming a homogeneous population |
| --ibdseg |
Infer IBD segments shared between any two samples using SNP data |
| --ibs |
Provide IBS statistics between any two samples using autosome SNP data |
| --invnorm |
Inverse normal transformation for quantitative traits prior to association scan |
| --kinship |
Estimate kinship coefficients between any two samples using SNP data |
| --lessmem |
Request less memory usage, now retired in KING 2.1.6 and later |
| --maxP |
Specify maximum p-values for being included in the output files |
| --mds |
SNP-based multi-demensional scaling (MDS) for ancestry inference |
| --model |
Specify a model template file for risk prediction |
| --mtscore |
GWAS scan with a many traits version of score test |
| --noflip |
Specify no-flip flag for risk prediction |
| --pca |
Compute principal components of ancestry using autosome SNP data |
| --pcs |
Specify the number of PCs used for PCA/MDS, e.g., 10 as default |
| --prefix |
Specify prefix of files for inference results, e.g., "king" as default |
| --prevalence |
Specify disease prevalence in the general population for risk prediction |
| --projection |
Project samples onto the principal component space of reference samples |
| --projection N |
Relatedness inference between two subsets where the first subset includes the first N samples |
| --related |
Fast and integrated relationship inference to identify close relatives |
| --risk |
Predict disease risk using genetic risk scores (GRS) |
| --roh |
Scan for runs of homozygosity |
| --rpath |
Full path of the R program. e.g., --rpath R |
| --rplot |
Plot inference results using R code |
| --sexchr |
Specify pair number of the sex chromosome for non-human species |
| --tdt |
GWAS scan with transmission-disequilibrium test |
| --trait |
Specify trait names for association scan |
| --unrelated |
Extract a subset of unrelated individuals |