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Missing documentation for the "LoF_info" "PERCENTILE"? #112

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MikeACG opened this issue Dec 27, 2024 · 0 comments
Open

Missing documentation for the "LoF_info" "PERCENTILE"? #112

MikeACG opened this issue Dec 27, 2024 · 0 comments

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@MikeACG
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MikeACG commented Dec 27, 2024

Hey there:

I have been unable to find any comprehensive explanation of what exactly is the "PERCENTILE" in the output of VEP (under "LoF_info"). I've tried looking around in the github and also the paper cited in the github but couldn't really find an explicit explanation. Particularly, how is this percentile calculated? Is it correlated or anti-correlated with the probability of a variant truly being LoF? The only hint I was able to find was in this issue here in the github where it is implied that a larger percentile decreases the probability of being LoF. I tried checking in a data driven way for enrichment of high percentile values in a set of common variants/low percentile values in a set of rare variants but my set of common variants is too small to say anything about this test I believe.

Am I missing some resource where these details are documented?
Thanks in advance.

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