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ANGSD / angsd

Program for analysing NGS data.
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Calculating Fst for windows with a fixed number of SNPs #548

Open EmilyPhelps opened 1 year ago

EmilyPhelps commented 1 year ago

Hello

I am trying to calculate the Fst for windows with a maximum number of SNPS e.g. windows have 100 SNPs.

I can do this from the raw a/ b values, but the problem is when I get to regions that have very few SNPS.

Is there a way in realSFS to specify a number of SNPs per window or a window of 50Kb, which ever comes first?

isinaltinkaya commented 1 year ago

Hi,

You can find details regarding windowed Fst estimations at http://www.popgen.dk/angsd/index.php/Fst#Sliding_Window_output.

Hope this helps.

Best, Isin