Hi all! I am trying to use the hl.de_novo function to call de novo variants. I am quite new to this, so can I get some insights if this function will suffice for making “good” calls, or if there is additional filtering that I should be doing prior to using the function?
Thank you very much !!
This function is supposed to be a general purpose de novo calling method, which uses the quality metrics and frequencies to build a statistical model of true positive probability. You shouldn’t need to filter ahead of time, though the method does not account for e.g. poor mapping quality of variants (you should filter to PASS ahead of time).
Thank you Tim! To clarify, will filtering to PASS before the test affect the statistical model (compared to not filtering)?
No. This model runs per-variant independently, so filtering on variants beforehand will remove results from the final output, but the statistical model is the same.