Data filtering

[gubrins]

Heys,

I'm using Dsuite to investigate if there was introgression in my dataset and I'm experiencing different results depending on the filtering settings (mainly in the amount of missing data and MAF filterings). I know that Dsuite allows missing data, but what should be the correct filterings for it? Depending on the percentage, the introgressions varies! There is an existing rule on the filtering parameters to use?

Thanks in advance, Gabriel

[gubrins]

I already found out what was my problem, but a new question arose. If I introduce in Dsuite as outgroup a species that diverged more than 5 MA and I run the test with and without missing data, do I get a general pattern in the first test and ancestral introgressions in the second one?

Thanks again!

[tanwei123456]

hello, gubrins, I also encountered the same problem as you when running Dsuite, that is, different filtering methods will get different results, may I ask how you solve it