Start fitting linear model for trait LDL ...
# of useful families for trait LDL is: 525; # of useful persons is: 525.
Association tests for trait LDL are finished.

Summary statistics for trait LDL have been saved in LDL.singlevar.score.txt.
Covariance matrices for trait LDL have been saved in LDL.singlevar.cov.txt.

Rare-Metal-Worker handled all individuals as unrelated.

The following parameters are in effect:

Input Files:
============================
--ped [sample2.ped]
--dat [sample2.dat]
--vcf [sample2.vcf.gz]

Output Files:
============================
--prefix []
--LDwindow [1000000]

VC Options:
============================
--vcShared [false]
--vcX [false]
--useCovariates [true]

Trait Options:
============================
--makeResiduals [true]
--inverseNormal [true]
--traitName [LDL]

Kinship Source:
============================
--kinPedigree [false]
--kinGeno [false]
--kinFile []
--kinSave [false]

Kinship Options:
============================
--kinMaf [0.05]
--kinMiss [0.05]

Chromosome X:
============================
xLabel [X]
xStart [2699520]
xEnd [154931044]

maleLabel [1]

femaleLabel [2]