Closed Daluser1 closed 2 years ago
Hi there,
Yes you can use ref/alt coding. You will lose a small amount of power without the anc/der information, but the statistics work perfectly well when using ref/alt.
-Zachary
Le lun. 17 janv. 2022 à 8:37 AM, Daluser1 @.***> a écrit :
Hi Dear Szpiech,
I am working on a dataset on which there is no information on the ancestral/derived state to encode 0 / 1 variants for analyses. I only have information from one population. I used ref/alt coding to calculate the statistics (iHS and nSL). However, I am not sure if these results are correct or not? I would sincerely appreciate any advice on it.
— Reply to this email directly, view it on GitHub https://github.com/szpiech/selscan/issues/69, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQSB43CHFGJAF3XH4YTUWQLSPANCNFSM5MEW4FRQ . 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 are subscribed to this thread.Message ID: @.***>
Dear Szpiech,
Thank you very much for your prompt reply. I have one more question: The ref/alt is by default being used by software? or, it should be specified in the command line?
It is the default (there is no other option). Hope this helps!
Zachary
Le lun. 17 janv. 2022 à 9:24 AM, Daluser1 @.***> a écrit :
Dear Szpiech,
Thank you very much for your prompt reply. I have one more question: The ref/alt is by default being used by software? or, it should be specified in the command line?
— Reply to this email directly, view it on GitHub https://github.com/szpiech/selscan/issues/69#issuecomment-1014599469, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQTDP3IZMVXH7M6S35TUWQRA3ANCNFSM5MEW4FRQ . 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 commented.Message ID: @.***>
Thanks Zachary for your reply. I appreciate it!
Dear Szpiech,
I am working on a dataset on which there is no information on the ancestral/derived state to encode 0 / 1 variants for analyses. I only have information from one population. I used ref/alt coding to calculate the statistics (iHS and nSL). However, I am not sure if these results are correct or not? I would sincerely appreciate any advice on it.