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Okay try adding the following parameters in the par file and then merge again. docheck: YES strandcheck: YES Also you can keep the PAM files as just .geno suffix. It will know that it’s PAM format.

Okay your individual file didn’t convert properly. Open the .fam file and change the -9 to a 1 or 2. Then convert it to PAM format again. Then merge with the AADR again.

Yes, I could see that you merged in PackedAncestryMap format – that’s why I thought it was quite unusual that you had the funny alleles as I’ve only ever seen that happen with Plink files. This is version 8 of Eigensoft you have just installed?

The "allele funny" errors usually only occurs if you merge two Plink files in mergeit since they require a more complicated process to flip snps which is done in Plink itself. It shouldn't happen if you merge two PackedAncestryMap or two Eigenstrat files since mergeit by default will check for...

Yes, the merging is done in either mergeit or Plink and is not dependent on AT. I would strongly recommend mergeit though as the Plink merge process is more complicated.

Latest version should be fine. Remember to first install latest version of R, and then R Studio. I use a Mac so there's no R Tools for me as it's Windows only. But as with the others I would recommend downloading the latest version.

Technically, AADR downloads are in PackedAncestryMap format – not Eigenstrat. So when you use convertf to convert the AADR files to Plink (aka PackedPed) you are converting from PAM, not Eigenstrat. And when users decide to convert "back to Eigenstrat" they are in actuality converting to it for...

Yes. Version 8.0 is the latest so best to download that one from your link and follow the instructions to compile. If you run into trouble you can try some pre-compiled older versions: https://github.com/chrchang/eigensoft

No, the convertf command is a part of the Eigensoft suite so you need to have that installed.

Okay I see the problem now. In your working directory it looks like you only have v62.0_1240k_public in PACKEDANCESTRYMAP format (similar to Eigenstrat). You need to convert it to PACKEDPED (Plink format) using ConvertF so you have the .bed, .bim and .fam files.

Yeah but put it in your merging command as well so it should be like: plink --allow-no-sex --bfile v62.0_1240k_public --bmerge mydata --make-bed --out v62.0_1240k_public_mydata

When merging you need the --make-bed flag before the --out flag to create the merged file.

The readme file that came with the v62.0 set implies that this is the most refined version: • "Twist" sequencing is a significant update in our protocol for capture and data for all newer samples are captured this way, as described in [RohlandMallickGenomeResearch2022]. These samples are...

Which pops did you use to set the eigenvectors?

link to v62.0 is here: https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/FFIDCW

I've noticed the massive size increase with Eigenstrat files as well. A thing to note is that the AADR downloads are actually in PackedAncestryMap format– not Eigenstrat. Both Eigestrat and PAM formats use the same file suffixes – .geno, .snp and .ind – but the only difference is with the .geno...

I've had some of the same issues merging in Plink which is why I tend to prefer merging in MergeIt which is generally more robust. However I find the v62.0 of the AADR is much more stable even when merging in Plink. BTW those warnings you've highlighted usually aren't a problem for uses...

To be honest I haven't used AdmixTools2 (or AT1) yet – I just know some things about how programs like these run. (I've been mostly working with ADMIXTURE up to now). However to change the population and/or sample names you edit the .ind file if you are using Eigenstrat or PackedAncestryMap...

Glad you got it sorted out. If you find it too slow to run you might want to move over to AdmixTools2.

Okay I just realised you are using (the original) AdmixTools. Those here are using AdmixTools2 which is a more streamlined version. AT2 also runs in R instead of shell. All the info you need to install and use it is here: https://uqrmaie1.github.io/admixtools/index.html