Hi Anurag - here, if you use R, try this... Let me know if it works

sorry, sent you a buggy one!

Try this one. It will plot Fst across all chromosomes (alternating point colors between chromosomes), highlight points that show significant Fst (FDR-corrected, or not, as you wish), and draw a loess-smoothed line (span adjustable). Or at least this is what it is supposed to do... Open RUN_ME_fstSmoother.R to try.

A big thank you. Yes it works.

Sincerely,

Anurag

does it work on your own data, though? (I was not sure about the input file format)

Yes, it worked on my data and the format of your example file was standard output file from Loistan. Thanks.

I have a question regarding filtering of p-value  -100 and 1. What does these signifies, especially 1, which I think is good outlier candidate.

Best,

Anurag 

You may do as explained on this page:

http://www.molecularecologist.com/2015/03/f-statistics-manhattan-plots-in-r/

and

http://www.gettinggeneticsdone.com/2014/05/qqman-r-package-for-qq-and-manhattan-plots-for-gwas-results.html

Let me know if it doesn't works