All Posterior_Prob are 0 when running PAINTOR without any annotations

[skanoni]

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]

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

[snlent]

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]

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]

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. — Reply to this email directly, view it on GitHub<#5 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AGIJTMG72ORMMORKAGGLWVLU3PQZ7ANCNFSM4DCWNHYA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[lanshanxuying]

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.