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gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data
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All Posterior_Prob are 0 when running PAINTOR without any annotations #5

Closed skanoni closed 7 years ago

skanoni commented 7 years ago

Hi, I am trying to run PAINTOR on small FM regions (~2000 variants) with dummy annotation files (0). When I get the results all Posterior_Prob are 0. I am not sure why this happening. I would appreciate some help. Thank you.

gkichaev commented 7 years ago

That's a bit strange. Are you sure your files are formatted correctly?

snlent commented 5 years ago

I see this issue was closed, but what was the resolution? I'm having the same problem. When I use a dummy annotation file and -enumerate k everything works fine, but when I use a dummy annotation file and -mcmc, all posterior probabilities are 0.

cindywen96 commented 2 years ago

I see the issue has been closed but is there an answer? I am having the same problem here. Some of my loci have all 0 PIP, while others look fine.

skanoni commented 2 years ago

Hi,

If I remember correctly I managed to resolved that by first filtering out all NAs from the LD matrix. I hope it helps.

From: Cindy Wen @.> Sent: 16 February 2022 17:59 To: gkichaev/PAINTOR_V3.0 @.> Cc: Stavroula Kanoni @.>; Author @.> Subject: Re: [gkichaev/PAINTOR_V3.0] All Posterior_Prob are 0 when running PAINTOR without any annotations (#5)

I see the issue has been closed but is there an answer? I am having the same problem here. Some of my loci have all 0 PIP, while others look fine.

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lanshanxuying commented 1 year ago

I see the issue has been closed but is there an answer? I am having the same problem here. Some of my loci have all 0 PIP, while others look fine.

I have the same issue like you . Did you solve this problem at last ? My LD matrix doesn't have any NAs.