Other Output Options
-check
-
Output marker quality checks to <inputfile>.CHECK
- -mendel
-
Output Mendel error information to <inputfile>.MENDEL
- -malehets
-
Output chromosome X male heterozygote information to <inputfile>.MALEHETS
- -dprime
-
Output
pairwise LD text table to <inputfile>.LD. Note that -dprime and
-check default to no haplotype output unless the -blockoutput flag is
also specified. - -png
-
Output PNG image file of LD display to <inputfile>.LD.PNG
- -compressedpng
-
Output low-resolution (smaller file) PNG image of LD display to <inputfile>.LD.PNG
- -svg
-
Output svg format of LD display to <inputfile>.LD.SVG
- -infoTrack
-
Include HapMap info track in PNG image outputs
- -spacing <threshold>
-
Use
proportional spacing for dumped LD pngs. <threshold> ranges from
0 (no spacing) to 1 (max spacing) with a default of 0. - -ldcolorscheme <type>
-
Use
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>
-
Only
output haplotypes with frequency ≥ <threshold>. Note that
multiallelic D' and htSNPs are computed using only displayed haplotypes. - -excludeMarkers <markers>
-
Exclude
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"