Data Check Options

-skipcheck

Skip all the genotype data quality checks and uses all markers for all analyses.

-minMAF <threshold>

Exclude
all markers with minor allele frequency below <threshold>, which
must be between 0 and 0.5. Default of 0. This option works in GUI mode.

-maxMendel <integer>

Exclude markers with greater than <integer> Mendelian inheritance errors. Default of 1. This option works in GUI mode.

-minGeno <threshold>

Exclude
markers with less than <threshold> fraction of nonzero genotypes.
<threshold> must be between 0 and 1 with a default of 0.5. This
option works in GUI mode.

-hwcutoff <threshold>

Exclude
markers with a Hardy Weinberg p-value less than <threshold>,
which ranges from 0 to 1 with a default of 0.001 This option works in
GUI mode.

-maxDistance <distance>

Maximum intermarker distance for LD comparisons (in kilobases). Default is 500. This option works in GUI mode.

-missingCutoff <threshold>

Exclude
individuals with more than <threshold> fraction missing data,
where <threshold> is a value between 0 and 1 with a default of
0.5. This option works in GUI mode.