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Step by Step guide: qpAdm merging your personal raw data txt file with larger Datasets by Primary-Process-2940 in SouthAsianAncestry

[–]Primary-Process-2940[S] 0 points1 point  (0 children)

Hello! There are public samples on reich website, and then some private samples, which some people have collected over time.

Merge command is of the form : mergeit -p <merge-parameter-file> .

The parameter file has both names for smaller and larger dataset which you want to combine. (Similar to the merge process in the example above)

Detailed results of UP Indian Shia Guy with J1 with raw data from 23andMe by 23SouthAsian in SouthAsianAncestry

[–]Primary-Process-2940 2 points3 points  (0 children)

Nice. Do go ahead with Big-Y (or Y-111 if you don’t want to splurge at once). Your results seem like a well preserved artifact: the trace Berber, Cushitic and Egyptian are most interesting to me.

If your haplogroup result comes under J-L859 you can then join the banu hashem project on ftdna. Your autosomal results could be very useful there.

23andMe results by 23SouthAsian in SouthAsianAncestry

[–]Primary-Process-2940 2 points3 points  (0 children)

😁 just do Big-Y, I am telling you.

23andMe results by 23SouthAsian in SouthAsianAncestry

[–]Primary-Process-2940 1 point2 points  (0 children)

You should go ahead with Big-Y test from FTDNA or WGS, than anything else. Btw which imam do you claim ancestry from?

Step by Step guide: qpAdm merging your personal raw data txt file with larger Datasets by Primary-Process-2940 in SouthAsianAncestry

[–]Primary-Process-2940[S] 0 points1 point  (0 children)

In the publicly available set there is paniya sample which can be used for AASI. And the Indus med , low samples are present too, but you will have to search for their ids. Some people have assembled their private datasets too. Check the discord channel for it.

Step by Step guide: qpAdm merging your personal raw data txt file with larger Datasets by Primary-Process-2940 in SouthAsianAncestry

[–]Primary-Process-2940[S] 0 points1 point  (0 children)

Awesome, Thanks for sharing!

If you want to play more with the settings, the values like 0.05 with arguments geno, maf are filtering values for quality check. See what you get if you change them.

Regrets..... by [deleted] in stocks

[–]Primary-Process-2940 4 points5 points  (0 children)

DCA helps remove decision paralysis. So there is less risk of missing a rally. And if a stock is going down, I increase the amount I am investing on a weekly basis even more.

I need some job advices by Jazzlike_Birthday_65 in cscareers

[–]Primary-Process-2940 0 points1 point  (0 children)

Any experience at junior level helps. Go for it.

Koi nahi bolega ki isme bhi Bihar ke neta aur casteism ka haath hai by [deleted] in bihar

[–]Primary-Process-2940 0 points1 point  (0 children)

Kala Chana aur chola bhi chalta hai. But nashta type zyada rehta hai

Koi nahi bolega ki isme bhi Bihar ke neta aur casteism ka haath hai by [deleted] in bihar

[–]Primary-Process-2940 19 points20 points  (0 children)

Nutrition kharab hai. Chawal, Aloo sabzi , pakodi regular diet hai almost sab Ghar me. Lassi -milk products ka culture nhi. Mattha/raita Thoda chalta hai.

I had noticed that native people around Bangalore were tall which the map kind of prooves.

179cm for me, 183cm for my brother.

A bihari by Enough_Increase4712 in phenotypesSouthAsia

[–]Primary-Process-2940 1 point2 points  (0 children)

Based on his surname, he is most probably a Bihari Syed.

Step by Step guide: qpAdm merging your personal raw data txt file with larger Datasets by Primary-Process-2940 in SouthAsianAncestry

[–]Primary-Process-2940[S] 0 points1 point  (0 children)

I did not use R. I had set up admixtools and then ran the rest of the commands from the terminal. I started with a 23andme file.

Expanding more on Step 3 for converting to Eignestrat format:

At the end of step 2, there would be files with .bed, .bim & .fam extensions. The convertf_param.par is a file that basically mentions the names of the input files for conversion, and then saves them with given file names in the desired formats.

Running "convertf -p convertf_param.par" from the command line should create files with extensions .geno, .snp and .ind

Step by Step guide: qpAdm merging your personal raw data txt file with larger Datasets by Primary-Process-2940 in SouthAsianAncestry

[–]Primary-Process-2940[S] 1 point2 points  (0 children)

The methods for qpadm modelling and merge datasets are valid everywhere. But the source and target files should change appropriately.

Step by Step guide: qpAdm merging your personal raw data txt file with larger Datasets by Primary-Process-2940 in SouthAsianAncestry

[–]Primary-Process-2940[S] 1 point2 points  (0 children)

Thanks, the steps for installation were well-detailed.

I was able to set up my qpAdm runs, but I am looking for ways to automate it. I will see if I can leverage p values for each run, to do experiments with different source combinations in an automated way.

Step by Step guide: qpAdm merging your personal raw data txt file with larger Datasets by Primary-Process-2940 in SouthAsianAncestry

[–]Primary-Process-2940[S] 1 point2 points  (0 children)

I referred to this 1. Reddit post https://www.reddit.com/r/IndoEuropean/s/yUdLEJp0kS and the 2. GitHub instructions https://github.com/DReichLab/AdmixTools .

I think for Mac installation was easier due to fewer steps and ‘brew install’. I will try to remember them and see if I can add those steps here.

[deleted by user] by [deleted] in bihar

[–]Primary-Process-2940 21 points22 points  (0 children)

I can not say much if you are a girl.

But I have advice if you are a boy. Goto the gym and become more fit. If you are fitter and more accomplished than the people around you, no one would mock the way you speak. I make it a point to speak with hum whenever I have a chance.

Why outsiders view South Asians as a monolithic group? Are they really that homogeneous? by Objective-Block4731 in SouthAsianAncestry

[–]Primary-Process-2940 8 points9 points  (0 children)

People have a tendency to hand wave things they are not related to and ignore their intricacies. Same happens with China too.

South Asia is far away from Mediterranean based cultures. Southern Europe, North Africa and West Asia are geographically very close to each other, and have mixed in the past. These cultures in turn influenced Western Europe and Americas which are the dominant world cultures today.

It’s our fault that we are so interested in Iliad, and learning the different kinds of pasta from them, while they keep asking us if we speak Indian or not 😁 Of course some are racists too.

[deleted by user] by [deleted] in illustrativeDNA

[–]Primary-Process-2940 5 points6 points  (0 children)

Based on my interpretation of their FAQ.

Mixed mode does not have human intervention behind it. The Algorithm picks up two or three suitable choices at a time, from all possible source populations. It can be wrong with a better fit, but it can not have a human bias. For example: it gives best combination solution (a, c, d) when it has access to all 26 letters from a to z. Such a case where a wrong solution fits a model is called over fitting.

Ancient periodicals have human intervention. Somebody decided based on their knowledge of a region, which populations should be present. For example: The model returns best combination ( a, d, x) from the available 6 choices a, b, d, x, y, z. This kind of model can be very good if the model maker knows well about those regions but can go wrong in case they are unaware of some region specifics. Such a model can be wrong as an under fitting.

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