search

zhanxw / rvtests

Rare variant test software for next generation sequencing data
131 stars 41 forks source link

AF is incorrect in SingleScore.assoc file #15

Closed jielab closed 7 years ago

jielab commented 7 years ago

Hi, I found that the AF column in the SingleScore.assoc file has negative values and positive values greater than 1. So, I think there is something wrong. Yesterday I recommended RVTESTS to a large audience of our consortium. Can someone please fix this issue before more and more others notice this issue?

Thanks!

Jie

zhanxw commented 7 years ago

Yes. I can replicate this problem. I need to fix it asap. Thanks! Xiaowei

On Apr 5, 2017, at 8:56 PM, jiehuang001 notifications@github.com wrote:

Hi, I found that the AF column in the SingleScore.assoc file has negative values and positive values greater than 1. So, I think there is something wrong. Yesterday I recommended RVTESTS to a large audience of our consortium. Can someone please fix this issue before more and more others notice this issue?

Thanks!

Jie

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

jielab commented 7 years ago

thanks, Xiaowei! Can you please fix this today and post an updated binary version online so that i could get the correct version and run quite some analyses over the weekend? A lot of people in our consortium just began to use RVTESTS, When they see this AF issue with negative numbers, they will somewhat lose confidence and might wonder if the other results are OK.

Best regards, Jie

jielab commented 7 years ago

Dear Xiaowei:

Can you please kindly let us know when the AF issue will be resolved?

Also, the log file always says that "connect() error: operation timed out". Don't know if this is a feature from "plink --no-web" that checks the PLINK version. It would be good to make this error message disappear if it is not really an error. Otherwise, analysts will be a little panic when they see "error" in the log file.

Thank you & best regards, Jie

jielab commented 7 years ago

still waiting to hear a timeline on when this AF issue could be fixed... thanks! Jie

zhanxw commented 7 years ago

I am working on that everyday. I estimate that the fix will be delivered by this week. Thanks.

On Mon, Apr 10, 2017 at 4:31 PM, jiehuang001 notifications@github.com wrote:

still waiting to hear a timeline on when this AF issue could be fixed... thanks! Jie

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/zhanxw/rvtests/issues/15#issuecomment-293085248, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJoiIyRugL0s-i9nrbMtKUXmdxV2A0qks5rup_FgaJpZM4M1BlG .

zhanxw commented 7 years ago

I think it's fixed in 5956f4c51b3fa2332f8f330d84d04346f5080751 Thank you.