KING INDEX (original) (raw)

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