Next
we will look at the parameter file param2, and its corresponding output file out2.dat. This file corresponds to having 50
burn-in and 100 follow-on iterations, with checkit = NO, details = YES and uses the badsnps file that we created in the previous step.
To do this type on the command line in the examples
directory:
|
>> ./ancestrymap
–p paramfile > outf& |
Compare
the output files outf
and out2.dat to make sure you can understand
the output generated. Note that the use of the random number generator makes it
impossible for the results to be exactly the same for two runs unless the
parameter seed has the same value. The
important things to focus on in this run are the t(Afr) and t(Eur) values, scores for
the various chromosomes and the genome log factor value.
In
addition to the standard output, this parameter file will also create a number
of output files in the outfiles
directory. These files are as follows, and have been discussed in detail in the
documentation.
§
act.out
§
freq.out
§
snp.out
§
theta.out
§
lambda.out
§
ethinc.out
§
ind.out