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how to handle ldsc with negative h2 value? #506

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SangGold opened this issue Jul 5, 2024 · 2 comments
Open

how to handle ldsc with negative h2 value? #506

SangGold opened this issue Jul 5, 2024 · 2 comments

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@SangGold
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SangGold commented Jul 5, 2024

when i run LDpred2 with gwas of biobank Japan for parkinson disease and target genotypes data is 504 samples of EAS in 1KGP, it raise an error: ldsc h2 estimate value is negative (h2 = -0.000936). I don't know why and how to fix it, could you help me resolve this problem?! Thank you so much!

@privefl
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privefl commented Jul 5, 2024

h2 estimates from ldsc can be negative, there is no error there; if you actually got an error, please report the precise error message
Then, either the trait you're looking at has a very very small heritability, or the matching between LD scores and chi square stats is incorrect.

@privefl
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privefl commented Aug 2, 2024

Any update on this?

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