Question: Sliding window analysis for angsd output
0
gravatar for wumy
6 months ago by
wumy0
wumy0 wrote:

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?

ADD COMMENTlink modified 6 weeks ago by axelwilhelm100 • written 6 months ago by wumy0
0
gravatar for axelwilhelm
6 weeks ago by
axelwilhelm100
Sweden
axelwilhelm100 wrote:

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

ADD COMMENTlink written 6 weeks ago by axelwilhelm100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1103 users visited in the last hour