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Did you download the associated .ind and .snp files? (Because you need all 3 to make it work in qpAdm). You don't open the .geno file. You reference the files you are using for your analysis in your qpAdm commands.

no problem. I'm planning on giving qpAdm a whirl myself in the next couple of months or so.

I found how to change the seed in qpAdm. However this is when running it with a parameter file but it looks like you a running it via R-scripts. The optional parameter you have to add (in the parfile) is, seed: Specifies the seed to be used. If set to 0, a random seed will be chosen...

Presuming everything is working the way it's supposed to, any result that meets the criteria (p-value threshold etc) is considered a plausible model. However I would be inclined to go with the more frequent result. Was the 2/10 result much different?

So you actually had to modify the code to set it to a static seed? I would have expected such a function to be already implemented as a user option in the software (e.g. by use of a flag). You also mentioned that it still occasionally gives an alternate result even with your set.seed in the...

I haven't used qpAdm (or any component of AdmixTools2) as of yet but from your description it most likely by default generates the seed randomly. I've been using ADMIXTURE which by default is set to a static seed but it's common practice in formal studies to generate the seed randomly by adding...

Any reason you aren't using Eigensoft MERGEIT to merge your individual file with the AADR data set (in Eigenstrat format)? It's much simpler and by default it does all the strand flipping and exclusions where necessary so you don't need to go through as many steps. Once you've created the...

I had a go mimicking the same process using PLINK i.e. merging my individual sample file with the AADR dataset (although I used an earlier version – v44.3_HO_public – which I already had in plink format) and although it merged (after the flipping and excluding etc), the genotyping rate was very...

No probs – I just found out in the meantime that the majority of ancient samples in the AADR data set have already been pseudo-haplodized. I even double checked by running a .freqx report on a subset of ancient samples in PLINK and they are all homozygous calls.

BTW do you know how to pseudo-haploidize the data? (preferably in PLINK or EIGENSTRAT format)

Thanks. I'd previously only seen the examples in the online PLINK 1.9 instructions. Yours was a bit different in that you did one flip and one exclude. I had been wondering what the benefit of merging in PLINK is when MERGEIT automatically checks and fixes strand incompatibilities during the...

Hi Jovialis, What do you mean by a one-sided merge in Plink? Also is there an issue with merging snps that aren't already in the AADR dataset? So far I've avoided Plink for merging because it always fails and I'd prefer not to go through the convoluted process to deal with the strand-flipping...

Yes, that's a fair observation about the age demographic and the fertility rate. I would also add the socioeconomic factor. But these things themselves are also to some extent a product of Islamic values and society (particularly their emphasis on having large numbers of children). That will...

According to 2021 demographics of Spain, Moroccans are 1.7% of the population. Thus looking at the crime stats above they are clearly overrepresented committing 8.5% of all crime, 2.5% of murders and 8.5% of sexual assaults. Contrast that with ethnic Spaniards who make up 84.8% of the...

Those results are quite consistent. I'm quite surprised, especially the Official Modern Averages keeping the same settings. When using any of the G25 Official calculators I have to really tweak the settings extensively (I was upgraded to PRO for more functions) to get accurate results. Those...

Are those the 'conservative results' for the Shared Modern Origins report? For your parents' results, was that from their own raw data files or from a phased file?

Also having lots of children is intrinsic to Islamic family life.

Some of my most accurate G25 results which correlate with my AncestryDNA results and/or genealogy. My genealogical calculation: 97% Irish, 3% English AncestryDNA results: 91% Irish, 7% Scottish, 2% English

Check my previous remark earlier in this thread. DNAGenics G25 coords aren't simulated (as in converted from other formats like K13 etc). They aren't the official IllustrativeDNA/Davidski coords but they are generated directly from your raw DNA file. They refer to them as 'synthetic coordinates'...

Douglas Murray in a recent interview: "10 years ago, what would you have thought about Sweden? You would probably have said 'Hot drinks, overpriced food, nice people, rather cold.' You wouldn't have said 'grenade attacks.'"