search

whitlock / OutFLANK

A procedure to find Fst outliers based on an inferred distribution of neutral Fst
18 stars 9 forks source link

Use OutFLANK with sliding-windows calculated Fst values #24

Closed Yung-Chien closed 4 years ago

Yung-Chien commented 4 years ago

Hi @DrK-Lo , @casalott and @whitlock , I'd like to find outlier of my Fst calculated by sliding-windows , and an issue appears that a window include many genotypes of many snps, it's hardly to difine a value like 0,1 or 2 to generate an input file for OutFLANK. So how could I create this input file? Thanks in advances, Yung

whitlock commented 4 years ago

Hi Yung,

OutFLANK isn’t designed (or suitable) for use on Fst calculated from sliding windows. The distribution of Fst from sliding windows is not a chi square as assumed by OutFLANK. So unfortunately I’d say it is unwise to try to use it for this case.

Michael Whitlock Department of Zoology University of British Columbia 6270 University Blvd. Vancouver, BC V6T1Z4 Canada

On Jul 5, 2020, at 11:59 PM, Yung-Chien notifications@github.com wrote:

 Hi @DrK-Lo , @casalott and @whitlock , I'd like to find outlier of my Fst calculated by sliding-windows , and an issue appears that a window include many genotypes of many snps, it's hardly to difine a value like 0,1 or 2 to generate an input file for OutFLANK. So how could I create this input file? Thanks in advances, Yung

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.