NAME

       smarteigenstrat - reduction of population bias for genetic analyses

SYNOPSIS

       smarteigenstrat  -i  <genotypefile>   -a  <indivfile>   -b  <snpfile>   -p  <pcafile>   -o
       <outputfile>      -l <logfile>  -k <numpca>  -q <qtlmode>

DESCRIPTION

       The program smarteigenstrat is part of EIGENSOFT.

       The EIGENSOFT package combines functionality from the group's population genetics  methods
       (Patterson  et  al.  2006) and their EIGENSTRAT stratification method (Price et al. 2006).
       The EIGENSTRAT method uses principal components  analysis  to  explicitly  model  ancestry
       differences  between  cases and controls along continuous axes of variation; the resulting
       correction is specific to a candidate marker's variation  in  frequency  across  ancestral
       populations,  minimizing  spurious  associations  while  maximizing  power  to detect true
       associations. The EIGENSOFT package has a built-in plotting script and  supports  multiple
       file formats and quantitative phenotypes.

OPTIONS

       -i     genotype   file  (PED,  PACKEDPED,  EIGENSTRAT,  ANCESTRYMAP  or  PACKEDANCESTRYMAP
              format)-o  output file (chisq)

       -l     logfile (screen output,including error messages)

       -q     YES for quantitative phenotype or NO otherwise

       For quantitative phenotype, sixth column of .ped file or third column of  EIGENSTRAT  .ind
       file  should  be  real  numbers.   For non-quantitative phenotype, sixth column of .ped or
       third column should be 'Case' or 'Control'

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.