Merging BED with v62 dataset with Google Colab

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Colab Notebook:- https://colab.research.google.com/drive/...sp=sharing

INPUT: .zip Plink Binary / PACKEDPED / BED
OUTPUT: Merged v62 Dataset

Merges entirely on Google Colab Runtime, nothing to do on Local System...
ETA: 5 hours

Adding support for analysis of Merged Dataset with Admixtools1, admixr, Admixtools2 soon...

If EIG file, use the optional step to upload and convert EIG to BED first and then proceed with the other steps...

@Kale @teepean

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Updated for some errors...

[TanTin]

Before to do the merge, let make sure you have the plink format of your data / bed, bim, fam/ data files.
To have these files you must convert from Eigenstrat format to plink.
This is required so you can use plink software for the next data processing.

[Inquirer]

I'm here.

[Inquirer]

I have RStudio and ADMIXTOOLS configuration files.

[TanTin]

Next step is to actually merge your plink datafile with the updated or new data..
For example we need to merge v62 Dataset with Takarkori samples.

The data for Takarkori was already posted here on the forum.
The best source for such converted data in this forum is teepean..
He already shared many such new data..
If you want the data from the official source : check on this link:
https://reich.hms.harvard.edu/datasets

So once you have the new data let see how to merge the new data with the existing dataset.

[Inquirer]

Next step is to actually merge your plink datafile with the updated or new data..
For example we need to merge v62 Dataset with  Takarkori samples.

The data for Takarkori  was  already posted here on the forum.
The best source for such converted data in this forum is teepean..
He already shared many such new data..
If you want the data from the official source : check on this link:
https://reich.hms.harvard.edu/datasets

So once you have the new data  let see how to merge the new data with the existing dataset.

I've downloaded the data from that link. Where can I get the Takarkori files here on the forums? Link?

[TanTin]

Now I am sharing my sripts for the merging.

Of course you will need to download the plink software.. Very simple executable file. No need to compile or what so ever..


So you have 2 choices: to merge directly from command prompt.. You run the command as Windows dos command.
Or you may integrate plink in your R studio environment.

This is my command from R-studio: ( example for merge)
system("plink --bfile For_merge/Dzudzuana/S2949_filtered --bmerge v52.2_1240K_public.bed v52.2_1240K_public.bim v52.2_1240K_public.fam --out GenoCenter/DataCentral_1.0 ")


This may look complicated, but it is not.
Let see what we do.

plink
--bfile For_merge/Dzudzuana/S2949_filtered
--bmerge v52.2_1240K_public.bed v52.2_1240K_public.bim v52.2_1240K_public.fam
--out GenoCenter/DataCentral_1.0

Now, here is my explanation:
plink is your executable file.
If you run this from command prompt, make sure you have this executable .exe file in your current directory..

bmerge - that means you use binarry compressed files or plink / bed.bim,fam / file
For other formats of data there is option with --file

--out ---> this is just the name of your output file. So you may select whatever name you want.

[TanTin]

https://zzz.bwh.harvard.edu/plink/

[TanTin]

Takarkori was already shared here somewhere on the forum.
Most of the time I get such data from the posts of our respected teepean..
Let see if I can find the original post and data from him. Otherwise I keep a copy of this data, that I can shate too.

[Inquirer]

Takarkori  was already shared here somewhere on the forum.
Most of the time I get such data from the posts of our respected teepean..
Let see if I can find the original post and data from him.  Otherwise I keep a copy of this data, that I can shate too.

I found a link on these forums for the Takarkori files: Link

However, it's behind a paywall.

[TanTin]

Takarkori  was already shared here somewhere on the forum.
Most of the time I get such data from the posts of our respected teepean..
Let see if I can find the original post and data from him.  Otherwise I keep a copy of this data, that I can shate too.

I found a link on these forums for the Takarkori files: Link

However, it's behind a paywall.

So I think I got the data from this post: (same post that you found)
https://genarchivist.net/showthread.php?...9#pid45809


I will share my copy of this data

[Inquirer]

Takarkori  was already shared here somewhere on the forum.
Most of the time I get such data from the posts of our respected teepean..
Let see if I can find the original post and data from him.  Otherwise I keep a copy of this data, that I can shate too.

I found a link on these forums for the Takarkori files: Link

However, it's behind a paywall.

So I think I got the data from this post: (same post that you found)
https://genarchivist.net/showthread.php?...9#pid45809


I will share my copy of this data

Okay, thanks.

[TanTin]

I found a link on these forums for the Takarkori files: Link

However, it's behind a paywall.

So I think I got the data from this post: (same post that you found)
https://genarchivist.net/showthread.php?...9#pid45809


I will share my copy of this data

Okay, thanks.

I had some account on https://ufile.io/,  but it seems to be expired.

[Inquirer]

So I think I got the data from this post: (same post that you found)
https://genarchivist.net/showthread.php?...9#pid45809


I will share my copy of this data

Okay, thanks.

I had some account on https://ufile.io/,  but it seems to be expired.

I guess I'll have to wait until I can get the files another way.