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szpiech / selscan

Haplotype based scans for selection
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Ancestral / derived alleles for iHS and nSL #69

Closed Daluser1 closed 2 years ago

Daluser1 commented 2 years ago

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.

szpiech commented 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.

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Daluser1 commented 2 years ago

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?

szpiech commented 2 years ago

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.

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Daluser1 commented 2 years ago

Thanks Zachary for your reply. I appreciate it!