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It's good numbers. Gz.

It's from southern arc.

40.6% Turkey Hellenistic I14472 + 59.4% Georgian. s.e. for both: 10.6% p-value: 0.32

I have a tutorial on this website.

admixtools2 (qpadm command).

results$weights # A tibble: 2 × 5 target left weight se z <chr> <chr> <dbl> <dbl> <dbl> 1 ponticgreek Turkey_Hellenistic_I14472 0.406 0.106 3.82 2 ponticgreek Georgian.DG 0.594 0.106 5.58 > results$popdrop # A tibble: 3 × 13...

Crap calculator.

Your command should be plink --allow-no-sex --23file jovialisrawdnafile.txt --make-bed --out jovialis After that you need to rename your sample which will be called ID001 in the .fam file (use a code editor) then filter.

Your I2a is from Karakachan paternal ancestor?

23ame V3 format has the highest coverage, you should use that or the all_SNPs option, the latter has some glitches I've noticed so v3 is the best (imo).

Try yseq clade finder for the updated nomeclature. I don't understand why people still use morley.

WGSExtract can produce a raw dna file with all SNPs from hg38. But, if you want to use the vcf you can use DNA kit studio that will convert it to 23afile txt that plink can read.

If you want some feedback, you are wasting your time. The highest SNP count possible you'll get with the Reich data is 1.24mil SNPs. You can hit that number easy if you extract a raw file from your BAM file. Then you can convert with plink.

Inconsistency errors are not taken into account in your work timeline. Your merge will be a dud if you haven't trimmed.

The results are similar if not identical. I use plink mostly with 2 on windows.

You don't have to convert the plink files to eigenstrat. admixtools2 reads plink files.

Nice work! :great: Looking forward to further discourse as more people get the hang of it.

Example, you can't make Turkey_BA work with Yamnaya (outgroup from Southern Arc): target left weight se z <chr> <chr> <dbl> <dbl> <dbl> 1 Turkey_EBA Turkey_N 0.425 0.0402 10.6 2 Turkey_EBA CHG...

Even if you use Yamnaya, the model fails for Turkey_BA, because there is no EHG for it to work.