Assigment of specific haplogroups

[cdquinto]

Hello, I'm using this program to assign haplogroups to some 1000 Genomes samples, but I am only getting the major haplogroups.

According to the paper: "YHap can be customized to either only assign to within the major haplogroups (A through to T), or all possible haplogroups at the finest level of classification." However I don't see where I can change this in the program.

Any help is greatly appreciated!

[Griffan]

Hi, I should have written readme more in detail. Currently, the best guideline is to follow the "autorun.advanced.pl" in rundir, which is a wrapper to search in branches you specified to.
Regarding your question, you can find in the script:

sub runJava()
{
    my ($model)=@_;
    my $cmdline="nohup sh ../../runYhap.sh ".$pop." ".$model." 1>&2 "." 2>>".$pop.".e.log";
    print STDERR "executing $cmdline ...\n";
    return system($cmdline);
}

the variable $model is where you should specify the specific branch you want to search, the more detailed branches you specified, the more the detailed assignment will be.
at the same time, for each run, the less complicated the model is, the more accurate the result will be.
you can find that in the "autorun.advanced.pl" script, the search started from ABCDEF these main branches, and in each next round, the model will be limited within the sub-branches of branches of previous round.

Hope this resolve your problem, feel free to contact me. I'm glad to help you successfully get your result.