Ancestral / derived alleles for CLR

[Daluser1]

Hello,

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 of VCF file to calculate CLR statistic. However, I am not sure if these results are correct or not? I would sincerely appreciate any advice on it.

[alachins]

Hi, You can directly use the VCF file with SweeD, which will do the CLR calculation correctly. Best regards, Nikos A.

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On Tue, Mar 15, 2022 at 11:44 PM Daluser1 ***@***.***> wrote: Hello, 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 of VCF file to calculate CLR statistic. 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 <#16>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCWEVHYR7SZ33CJI4SLVAEHFVANCNFSM5Q2ERG4Q> . 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: ***@***.***>

-- Nikolaos Alachiotis

[Daluser1]

Hi,

Thank you very much for your reply. However, using VCF what information is being used instead of ancestral/derived to calculate CLR?
Best Regards,