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Thread: ancIBD
Post: RE: ancIBD
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Queequeg Wrote: (Yesterday, 04:46 PM)
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Angles: if I'm right, you have anyways confirmed the connection between DA238, the most eastern shifted sample of the Levänluhta group and NEO61 of the BOO si... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
10 hours ago |
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Thread: ancIBD
Post: RE: ancIBD
| Precisely:
https://i.imgur.com/QKMxfpP.jpg
You see that when I say "no significant genealogical link" I am being a bit disingenuous. Let's just say I was hoping for something else... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
Yesterday, 11:53 AM |
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Thread: ancIBD
Post: RE: ancIBD
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AimSmall Wrote: (Yesterday, 12:58 AM)
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Any insights it has shown you?
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I haven't started using it systematically yet. My first attempts were more akin to the disordered behaviour of a child who... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
Yesterday, 06:32 AM |
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Thread: ancIBD
Post: RE: ancIBD
| There it's finished. The 22 hdf5 files are snug in their box called “Allentoft_IBD”. I just spent an hour editing IBD stats all over the place. It's straightforward and blazingly fast. What a wonderfu... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
05-17-2024, 02:04 PM |
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Thread: The Genetic Origin of the Indo-Europeans
Post: RE: The Genetic Origin of the Indo-Europeans
| Hi Ffoucart! Nice to see you on GA! |
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Anglesqueville |
Ancient (aDNA)
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279 |
21,097 |
05-15-2024, 11:13 AM |
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Thread: ancIBD
Post: RE: ancIBD
| I apologize, there were 2 critical typos in my little guide: in a command, I wrote "FORMAT" in place of "INFO". This is now corrected. |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
05-15-2024, 06:08 AM |
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Thread: ancIBD
Post: RE: ancIBD
| Guide
1) Familiarization with the program
a) Of course all this is done under LINUX. For me it is UBUNTU. I don't see why there would be problems with other LINUXes, but I can't guarantee it.
b) ... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
05-14-2024, 09:15 PM |
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Thread: ancIBD
Post: RE: ancIBD
| The hdf5 file for chromosome 1 and all imputed individuals from Allentoft is 780 Mb, so it's perfectly usable. You know that the mass is said once the HDF5s have been produced. This conversion on such... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
05-14-2024, 04:45 PM |
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Thread: ancIBD
Post: RE: ancIBD
| Cejo: It's complicated and I still need to do some checking. Precisely at the moment, I am looking at whether it is practically feasible to run ancIBD on the complete imputed data from Allentoft, or w... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
05-14-2024, 03:24 PM |
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Thread: ancIBD
Post: RE: ancIBD
| https://www.youtube.com/watch?v=IUZEtVbJT5cAnd finally .... Champagne! It works! |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
05-14-2024, 02:17 PM |
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Thread: Backyard Hobbies
Post: RE: Backyard Hobbies
| I live in a fairly remote corner of the Pays de Caux, in the hinterland of Etretat, on approximately 1 hectare bordered by fields. At the bottom of my domain there is a group of beech trees, very old ... |
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Anglesqueville |
The Lounge
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17 |
436 |
05-13-2024, 08:12 PM |
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Thread: Dataset merging help
Post: RE: Dataset merging help
| Genetics189291, I'm seemingly on your ignore list. I can't therefore reply to your PM. I guess you want to convert from PLINK to EIGENSTRAT? If this is correct, the word “CONTROL” appears in the indiv... |
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Anglesqueville |
Inquiries Corner
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12 |
296 |
05-07-2024, 02:20 PM |
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Thread: R1b-L51 in Yamnaya: Lazaridis 2024
Post: RE: R1b-L51 in Yamnaya: Lazaridis 2024
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Sephesakueu Wrote: (05-06-2024, 11:06 PM)
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rmstevens2 Wrote: (05-06-2024, 07:58 PM)
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Sephesakueu Wrote: (05-06-2024, 03:25 PM)
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I dont know how you missed all the fuss about J-L283 in this fo... |
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Anglesqueville |
R1b-L51
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398 |
14,433 |
05-07-2024, 06:24 AM |
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Thread: ancIBD
Post: RE: ancIBD
| Well, for once my optimism was premature. Everything goes well on the first three chromosomes and then goes wrong. I don't have the slightest idea what the problem is. No champagne yet (I don't like c... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
05-05-2024, 04:24 PM |
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Thread: ancIBD
Post: RE: ancIBD
| Okay, I've made progress. Receiving no response from Ringbauer, I embarked on an enterprise that seemed a bit hopeless. I reduced the Allentoft vcfs to the vital minimum (the GT and GP fields resultin... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
05-05-2024, 07:11 AM |
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Thread: What Are You Listening To
Post: RE: What Are You Listening To
| https://www.youtube.com/watch?v=wxRailcznHE
First: this quartet is one of the greatest works of the early 20th century, and one of the pinnacles of chamber music, all eras combined. Second: I don't k... |
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Anglesqueville |
The Lounge
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196 |
9,919 |
05-04-2024, 08:18 PM |
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Thread: ancIBD
Post: ancIBD
| Do any of you have experience with the ancIBD program? In case yes, here is my problem. I installed the software on my Linux machine without a problem. I ran the exemple files provided without any pro... |
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Anglesqueville |
Inquiries Corner
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16 |
521 |
04-28-2024, 02:48 PM |
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Thread: Uralic populations in the qpAdm models by Zeng et al. 2023
Post: RE: Uralic populations in the qpAdm models by Zeng...
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Jaska Wrote: (04-23-2024, 03:50 PM)
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But then, considering your models for the Levänluhta population, how is the Minino ancestry divided between the CWC and the direct EHG ancestries?
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right p... |
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Anglesqueville |
Ancient (aDNA)
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32 |
1,949 |
04-25-2024, 04:46 PM |
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Thread: Uralic populations in the qpAdm models by Zeng et al. 2023
Post: RE: Uralic populations in the qpAdm models by Zeng...
| ^^Kale, I wanted to stick as closely as possible to Zeng, so in particular I took his right list trying to give it a less extravagant size, but without adding anything (except, I seem to remember havi... |
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Anglesqueville |
Ancient (aDNA)
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32 |
1,949 |
04-23-2024, 04:40 PM |
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Thread: Uralic populations in the qpAdm models by Zeng et al. 2023
Post: RE: Uralic populations in the qpAdm models by Zeng...
| The right List is Zeng's but reduced to what seems to me to be not completely useless (although we could reduce it further). As always I use Admixtools (and not Admixtools 2), qpfstats, allSNPs = YES.... |
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Anglesqueville |
Ancient (aDNA)
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32 |
1,949 |
04-23-2024, 02:34 PM |
