smarteigenstrat - reduction of population bias for genetic analyses

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

smarteigenstrat 6.1.2                               July 2016                                 SMARTEIGENSTRAT(1)

       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.

       smarteigenstrat - reduction of population bias for genetic analyses

-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'

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