I was wondering what is the best protocol for getting accurate sex chromosomes copy number predictions?
Currently I have a pool for normals of mixed gender which I am passing into the
reference function. I don't set the
-y option to create a male reference. There appears to be no option to actually give the gender of the various input coverage files. Yet if you use the
-y option, the manual says:
Create a male reference: shift female samples' chrX log-coverage by -1, so the reference chrX average is -1. Otherwise, shift male samples' chrX by +1, so the reference chrX average is 0.
I assume that it automatically detects the gender and accounts for their sex chromosomes? Or is there a way to pass in the exact gender of each input normal sample?
I then use this pooled reference to then call
fix, and then when it comes to the
call function there is the
-g option to specify the gender of the input sample, unlike the
Is there any critical steps that I am missing to getting accurate sex chromosome copy number predictions?