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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
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kolompar Wrote: (03-09-2025, 03:05 PM)
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150k SNPs out of 1240k were chosen where South African is derived and Denisovan is ancestral so no wonder South African and Denisovan affinity are inversely ... |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-25-2025, 06:58 PM |
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Thread: X Chromosome false-positive calls as Y
Post: RE: X Chromosome false-positive calls as Y
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mjaguk Wrote: (03-24-2025, 06:24 PM)
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@TanTin
I have some of the SNPs you mention in your post #8 - about a quarter of them.
With me having over 1,000 of these false Y SNPs in my Nebula VCF f... |
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TanTin |
X Chromosome (X-DNA)
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25 |
797 |
03-25-2025, 02:01 AM |
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Thread: X Chromosome false-positive calls as Y
Post: RE: X Chromosome false-positive calls as Y
| You may compare the position number (Build37) with the positions that I provided in my post #8.
(If your positions are in Build38 - it must be converted to Build37 .)
As I explained: I suspect it... |
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TanTin |
X Chromosome (X-DNA)
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25 |
797 |
03-24-2025, 11:48 AM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
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AimSmall Wrote: (03-22-2025, 12:06 AM)
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Going to leave this right here...
https://genarchivist.net/showthread.php?tid=95&pid=48722#pid48722
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I am not sure about this new model.
It is based ... |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-23-2025, 11:11 AM |
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Thread: Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility
Post: RE: Postglacial genomes from foragers across North...
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teepean Wrote: (03-20-2025, 10:06 AM)
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Coverage
Code:
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FID IID MISS_PHENO N_MISS N_GENO F_MISS
1 I32545 N 83274 1196712 0.06959
2 I32552 ... |
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TanTin |
Ancient (aDNA)
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22 |
1,253 |
03-20-2025, 09:36 PM |
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Thread: Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility
Post: RE: Postglacial genomes from foragers across North...
| Here is my PCA projection with the new data: ( new Uralic data in yellow ). |
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TanTin |
Ancient (aDNA)
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22 |
1,253 |
03-20-2025, 06:45 PM |
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Thread: Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility
Post: RE: Postglacial genomes from foragers across North...
| The quality of the new samples is not bad at all. This is the missingness. (percent of the missing snips , example: 0.47 = 47% missing variants) |
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TanTin |
Ancient (aDNA)
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22 |
1,253 |
03-20-2025, 06:30 PM |
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Thread: Smartpca (beta testing)
Post: RE: Smartpca (beta testing)
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Genetics189291 Wrote: (03-15-2025, 10:20 PM)
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AimSmall Wrote: (03-15-2025, 09:04 PM)
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Can you elaborate on this statement, "convert back two eigenstrat"?
What does that mean?
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Nomad data ... |
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TanTin |
Autosomal (auDNA)
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72 |
3,001 |
03-15-2025, 11:31 PM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
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AimSmall Wrote: (03-15-2025, 02:42 PM)
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I find 589,245 matching positions between the two.
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Make sense. 50 % of 1240k snips .
The same percentage that I found for CHR 15. |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-15-2025, 02:58 PM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
| What you need to match is the 4-th column - the position number. |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-15-2025, 02:00 PM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
| It is the same format.
Just the name of the snips are different.
In 1240k the name is rsxxxxxx , where xxxxxx is the position number. ( but it could be also different number)
The other dataset is ... |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-15-2025, 01:57 PM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
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kolompar Wrote: (03-09-2025, 03:05 PM)
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150k SNPs out of 1240k were chosen where South African is derived and Denisovan is ancestral so no wonder South African and Denisovan affinity are inversely ... |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-15-2025, 04:07 AM |
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Thread: Another dataset of high coverage shotgun genomes, courtesy of Ranis
Post: RE: Another dataset of high coverage shotgun genom...
| Checking for all snips on CHR15:
dataset Ranis: 215k
dataset 1240k: 36k
Shared snips: 18.7k
The number of shared snips is 50% of dataset 1240k or ~9 % of dataset Ranis .
However when we a... |
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TanTin |
Ancient (aDNA)
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19 |
1,231 |
03-15-2025, 02:44 AM |
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Thread: Another dataset of high coverage shotgun genomes, courtesy of Ranis
Post: RE: Another dataset of high coverage shotgun genom...
| I did additional verifications on " high coverage shotgun genomes" or Ranis "genome-wide shotgun data" ...
https://edmond.mpg.de/dataset.xhtml?persistentId=doi:10.17617/3.EGKV28
I applied some ... |
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TanTin |
Ancient (aDNA)
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19 |
1,231 |
03-15-2025, 02:30 AM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
| https://pmc.ncbi.nlm.nih.gov/articles/PMC11839475/
Supplementary Figure 12.3: Model estimates from momi2 for the simpler model (PNG model) in which
Yorubas (YRI), Han Chinese (CHB), an introgressi... |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-14-2025, 05:11 PM |
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Thread: Another dataset of high coverage shotgun genomes, courtesy of Ranis
Post: RE: Another dataset of high coverage shotgun genom...
| I'd like to share with you this report for CHR17.
Here is an example for Denisova/Neandertal variants among AMH.
There are 2 options only: people have the ancient ancestral segment matching to D/... |
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TanTin |
Ancient (aDNA)
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19 |
1,231 |
03-13-2025, 03:21 AM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
| Yes, you right ! This was our previous conversation for the same dataset:
https://genarchivist.net/showthread.php?tid=1371&highlight=ranis+dataset
So I got the dataset and converted it during that t... |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-13-2025, 01:44 AM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
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AimSmall Wrote: (03-12-2025, 11:07 PM)
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Ugggh.... is this the Ranis dataset? Was about to convert it to plink when something started to feel familiar.
If so, good dataset. Just got excited thi... |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-12-2025, 11:43 PM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
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kolompar Wrote: (03-10-2025, 12:44 PM)
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Yes if Denisova is ancestral then the stat is 0 and if SA and Neanderthal are derived then you have inverse relation and there's an artificially higher numbe... |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-12-2025, 07:09 PM |
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Thread: Neanderthals data converted
Post: RE: Neanderthals data converted
| There is this dataset with 8M snips
https://edmond.mpg.de/dataset.xhtml?persistentId=doi:10.17617/3.EGKV28
294 individuals included, including also Chimp, Denisova and few Neandertals.
In case is... |
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TanTin |
Ancient (aDNA)
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90 |
3,880 |
03-11-2025, 10:07 PM |
