Parameter Setting

[lile19920725]

HI Robbie,
I had two questions：
1，For a relatively small sample (4-40 individuals), with ~1X per-sample，How to set parameters k and nGen(for 4 samples，k=4 and nGen=20)？
2，How to set filter parameters after impution？
Thanks!
Lee

[rwdavies]

Hi Lee,
In general that is far fewer samples than I would recommend. I would start with K=2 and see how it performs, and then maybe for upwards of the 40 case, try K=2 or K=3.
For filtration, without any other evidence which would suggest particular thresholds, I normally suggest filtering pretty much exclusively based on the INFO scores, e.g. keeping INFO>0.4 as the only filtration
Best wishes,
Robbie