Other Output Options


Output marker quality checks to <inputfile>.CHECK


Output Mendel error information to <inputfile>.MENDEL


Output chromosome X male heterozygote information to <inputfile>.MALEHETS


pairwise LD text table to <inputfile>.LD. Note that -dprime and
-check default to no haplotype output unless the -blockoutput flag is
also specified.


Output PNG image file of LD display to <inputfile>.LD.PNG


Output low-resolution (smaller file) PNG image of LD display to <inputfile>.LD.PNG


Output svg format of LD display to <inputfile>.LD.SVG


Include HapMap info track in PNG image outputs

-spacing <threshold>

proportional spacing for dumped LD pngs. <threshold> ranges from
0 (no spacing) to 1 (max spacing) with a default of 0.

-ldcolorscheme <type>

a particular color scheme for dumped LD pngs. <type> can be
DEFAULT, RSQ, DPALT, GAB or GAM. More information can be found with the
LD display help

-hapthresh <threshold>

output haplotypes with frequency ≥ <threshold>. Note that
multiallelic D' and htSNPs are computed using only displayed haplotypes.

-excludeMarkers <markers>

markers in a comma separated list with ranges specified as start..end.
So, to exclude markers 3, 5 and 10 through 15 you'd use
"-excludeMarkers 3,5,10..15"