Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Calculating r^2 in vcftools for only one SNP? nk Bioinformatics 8 08-01-2014 01:55 AM
where to find coordinates for promter, splice site, splice regulatory site? cliff Bioinformatics 13 11-18-2013 05:23 PM
Understanding PAML output according to site/branch/branch-site models used mdeloger Bioinformatics 1 11-15-2012 03:21 AM
Calculating Ti/Tv ratio Heisman Bioinformatics 4 05-04-2012 08:11 AM
calculating the coverage lyz1030 Bioinformatics 3 04-03-2012 05:03 PM

Thread Tools
Old 03-10-2020, 12:40 AM   #1
Junior Member
Location: Singapore

Join Date: Mar 2019
Posts: 5
Default Calculating per site Dxy

Hi everyone,

I am trying to calculate Dxy per site between two populations from ANGSD output. I am using the CalcDxy.R script from NGSpopgen for this purpose. I seem to be getting really high Dxy estimates for all my SNP sites, these are very different from the Fst estimates of the same comparison. I have attached a manhattan plot to illustrate this.

Other than quality filters, I have used SNP_pval 1e-6 and skipTriallelic 1 during SNP calling.

Does anyone have any idea as to why I am getting numbers like this?
Attached Images
File Type: jpg Screenshot 2020-03-10 at 4.37.25 PM.jpg (80.2 KB, 0 views)
pitch_ is offline   Reply With Quote

angsd, dxy, ngspopgen

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 04:35 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO