R1a L657 in Roopkund lake, Uttarakhand from 800CE, but no Steppe

In 2019, a paper¹ was published with the analysis of the remains of 38 individuals whose bones were found in Roopkund lake, Uttarakhand at an altitude of 5000m above sea level. 

Context of Roopkund Lake. a Map showing the location of Roopkund Lake. The approximate route of the Nanda Devi Raj Jat pilgrimage relative to Roopkund Lake is shown in the inset. b Image of disarticulated skeletal elements scattered around the Roopkund Lake site. Photo by Himadri Sinha Roy. c Image of Roopkund Lake and surrounding mountains. Photo by Atish Waghwase

Integrating raw DNA data into aDna database for use in Admixtools

Representative example of a user's data being merged into Eigenstrat format for Admixtools

I have gotten quite a few enquiries already from people wanting to merge their raw data (from AncestryDNA, FTDNA, LivingDNA, MyHeritage or 23andMe) into the aDna eigenstrat database so they can use it for qpAdm analysis of their own after reading my qpAdm 101 tutorial. I want to help, but converting merging etc is a time consuming process and a bit complicated.

I could possibly do it for 2-3 people a day. In case some people don't have linux or don't want the hassle of running the programs themselves, I could even run 4-5 models suggested by them for a fee.

Let me know in the poll and also the comments if its something you guys will be interested in. With the virus lockdown affecting my business sector, I have got some extra time on my hands.

Update: 

Since I already have 2-3 people wanting their data merged and get the eigenstrat file for personal use, I have decided to go ahead and open it up for all.

HOW TO Part 2:: How to test models using qpAdm - qpAdm 101

qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. I hope this tutorial helps people interested in doing own research as qpAdm validated models which are constructed well provide a high standard of evidence to the model.

qpAdm is used to validate models that are fed into it by the user. The details that need to passed to the qpAdm program are as follows.

1. Target population
2. List of 2 or more source populations 
3. List of Right populations or Right Pops.
4. The populations in 1 & 2 are together called Left Populations or Left Pops and the first population in this list is considered as target population by qpAdm.
5. The first population among the right pops has to be a basal population (Outgroup) and usually an african population like Mbuti, ShumLaka or Mota etc is chosen for this purpose.

A standard example of a qpAdm model is 

 Target population (Target) = source population 1 (Source 1) + source population 2 (Source 2) 

The qpAdm output will contain a p-value (also called tail probability or tailprob), admixture coefficients x & y for Source1 and Source2 respectively such that x+y = 1 (or 100%) and standard errors for those coefficients. 

Stepwise tutorial to Install Admixtools & Plink

 I will make 3 separate posts on how to install Admixtools, run qpAdm and run qpGraph respectively. This first blog post will detail steps to successfully install Admixtools by Harvard lab.

STEP 1.  Have a Linux system

Admixtools cannot be run from a Windows system. If you have a Windows or MacOS Host system, install Oracle VirtualBox from here. Its free.

Install any Guest linux system on this VBox. I use OpenSuse Leap v15.1 for no particular reason apart from that I'm used to it. The virtual image for installation can be downloaded for free from here.

Once this is done, install the guest Linux system on the VBOX. This video below can guide you. 

In the Virtual box settings (can only edit it when Guest OS is shut down), make sure to use 2 processors, 3d acceleration enabled in display settings and I would suggest using 4GB RAM. Use VBoxSVGA as Graphics controller in display settings so that you can get full screen display in guest OS.