I was trying to estimate the minimum sequencing depth required to confidently detect somatic variant using Poisson distribution based variant caller (such as somatic variant caller or Pisces from illumina).

Power analysis is used which requires significance level (0.05), power / sensitivity (99%) and effect size to estimate sample size (sequencing depth). I am not sure how to calculate the effect size in such context. Can anyone share some insight? Thanks a lot.

  • $\begingroup$ It's standard stats, it's a while since I've done this, but it's textbook stuff $\endgroup$ – Michael Jul 19 '19 at 8:41
  • $\begingroup$ Try running a pilot study to get some preliminary results you can use to estimate the effect size = difference / SD. $\endgroup$ – TheSimpliFire Jan 6 at 15:16

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.