Reccomended parameter settings for whole chromosome of genotype-density data

[sahwa]

Hi,

I'd like to run iSAFE on a single chromosome (6), containing ~70K individuals, 35,863 SNPs covering 170Mb. I've been trying lots of different parameter settings of different window sizes, minimum region sizes etc, but can't seem to find an optimum set that will work.

What would you recommend to get the optimum results in this scenario?

Thanks,

Sam

[alek0991]

Dear Sam,
Could you please share a few parameter set you have tested and the outputs?
Best,
Ali