What exactly is the 'p' in PLINK --thin?

Question

[dani.mag.fernandes]

Hello. I have tried to find a clear explanation of what the probability p in PLINK --thin corresponds to. Is it simply the probability of each variant to be kept during the filtering, or does that probability take anything else into consideration? For example, with --thin 0.15, each variant has a 15% chance of being kept?

Answer 1

[chrchang523]

From https://www.cog-genomics.org/plink/1.9/filter#thin : "--thin removes variants at random by retaining each variant with probability p". You can find this link from e.g. https://www.cog-genomics.org/plink/1.9/index .

"plink --help thin" also gives you this information.