angsd Fst outlier
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21 months ago

I have used angsd to estimate Fst values for sliding windows between pairs of populations (3 populations total). I wish to determine which Fst values are outliers. Is there a way to do this within angsd? I'm working with low coverage genomes and genotype likelihoods.

Output looks like: region chr midPos Nsites Fst01 Fst02 Fst12 PBS0 PBS1 PBS2 (94,130)(20899,39240)(10000,60000) chr1 35000 38 0.447652 0.234849 0.388338 0.184842 0.408735 0.082841 (94,130)(20899,39240)(20000,70000) chr1 45000 38 0.447652 0.234849 0.388338 0.184842 0.408735 0.082841 (105,130)(32159,39240)(30000,80000) chr1 55000 27 0.519858 0.239442 0.468049 0.188086 0.545587 0.085617 (131,131)(92641,92641)(50000,100000) chr1 75000 2 0.389971 0.036278 0.161695 0.177414 0.316835 -0.140461

Where each Fst column is a weighted Fst value for a specific window between pairs of populations.

angsd fst outlier manhattan pvalue • 789 views
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