Sliding window analysis for angsd output

Question

[wumy]

Hi everyone,

I am trying to do a sliding window analysis on my dxy output from ANGSD. My data is whole-genome and I have calculated dxy for all chromosomes using calcDxy.R in the ANGSD script folder. I have obtained a file with 3 columns: Position, Dxy, Chromosome. I have around 11 million SNPs, thus 11 million Dxy values in the text file.

I would like to do a sliding window analysis of 50K bp window and 10K step on the dxy output file. Does anyone have any idea how to accomplish this?

Answer 1

[axelwilhelm]

Matteo Fumagalli has this tutorial

https://github.com/mfumagalli/ngsTools/blob/master/TUTORIAL.md

It has a section about nucleotide diversity with sliding window R scripts