<p>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).</p>

<p>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.</p>

CC BY-SA 4.0
2019-07-19T08:41:36.583Z
It's standard stats, it's a while since I've done this, but it's textbook stuff
M__
CC BY-SA 4.0
2020-01-06T15:16:37.667Z
Try running a pilot study to get some preliminary results you can use to estimate the effect size = difference / SD.
TheSimpliFire
<variant-calling>
Effect size in power analysis when dealing with Poisson based variant caller
# Effect size in power analysis when dealing with Poisson based variant caller

(Asked by: username_0 on 2019-07-19)

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.

**Tags:** variant-calling
> **Comments:**
> **username_1**: It's standard stats, it's a while since I've done this, but it's textbook stuff  
> **username_2**: Try running a pilot study to get some preliminary results you can use to estimate the effect size = difference / SD.  

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## 0 answers

