I realize PL will be normalized in this page.
However, I need the data before normalize, raw PL, where can I get it?
Thanks for your help.
Ah, I see. I think you will find it easier to navigate the code with an IDE like IntelliJ. The code you want starts in calculateGLsForThisEvent() in HaplotypeCallerGenotypingEngine.java, which calls calculateLikelihoods in InfiniteRandomMatingPopulationModel.java. From there if you're using an IDE you can explore the code. We cannot provide more support than this. Good luck!
That data is not output, sorry. You would have to modify the program to do so.
Can you tell me which function should I change?
This is actually a fairly complicated question -- I can't answer that easily. Are you familiar with java programming?
yes, I am familiar with java, but there are too many function that I cannot find which I should modify.
Should I need to link the Github?
Because I cannot link it successfully.
What do you mean by "link the github"? Do you mean download the source code?
No, Shelia post a Github link above my question.
I though it is about the function of "raw PL". isn't it?
I have downloaded the source code but I cannot find the function
Hi, Geraldine. I have a way to get the raw PLs by the observed PLs (like, 31,223,0).
rawPL1 = 31+rawPL3 = -10log(p1)
rawPL2 = 223 + rawPL3 = -10log(p2)
rawPL3 = -10*log(1-p1-p2)
by these three equations, we can get the rawPL3, p1 and p2.
I don't know if this is correct, your guidance is important for me.
I think this article will help you.