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

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?

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updated by chrchang523 chrchang523 • written by dani.mag.fernandes • dani.mag.fernandes

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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.

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written by chrchang523 chrchang523

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