SAS Code for generating a LOD score with Proc Mixed:
/*y: trait; alpha-alpha13:indicator
variables of the parental lines of the RIX observations; m1-m382: total 382 markers considered*/
/*To use this file for your data analysis, you need to change the 
corresponding number of parental RI lines (which is 13 in this file) and
the total number markers you have (which is 382 in this file).*/
data a;
infile ‘qtl.dat' missover;
input y alpha1-alpha13 m1-m382;
%Macro doloop;
%do j=1 %to 382;
ods output tests3=ftest&j;
proc mixed data=a;
class m&j;
model y = m&j;
random alpha1-alpha13/type=TOEP(1);
quit;
data ftest;
set ftest ftest&j;
run;
%end;
%mend;
%doloop;
data _null_;
set ftest;
file ‘qtl.output';
put fvalue ProbF;