There is easy way how to avoid this.
You have to filter the samples being merged to the large dataset to only those SNPs already existing in the large dataset, else the extraneous SNPs in the sample that don't occur in the large forces the large to add No Calls to every sample in it swelling...
There was a recent publication claming similar not too far ago.. So this ChatCPT creation is a good example of Google Search . You posted this in another topic as well. Next time when you use ChatGPT do also your own search with Google or other search engines to see who is the original source...
What is the question ? You did not share your own results on G25 and I don't see what is your good fit. Regarding G25 the best place to ask is Davidsky at his blog Eurogenes.
This is not a good idea to use *.ped as extention for the parameter file. You may use .txt or .par instead.
.ped is used for packed eisenstrat file format.. Just try to avoid that kind of mess. In the original software from git hub or downlowad there are excelent examples for parameter files...
Actually - you don`t need that much 100GB for the conversion. But you need lot of RAM on you computer. The conversion may take some time, may be half an hour or more. On slow computer it may not run at all or may freeze.The result from geno to ped will generate the same size file , near 5 GB...
Yes, both convertions are possible. The templates for parameter files are provided with Eigensoft:
https://github.com/argriffing/eigensoft/tree/master/CONVERTF
echo "
genotypename: full230.geno
snpname: full230.snp
indivname: full230.ind
outputformat: PACKEDPED
genotypeoutname: full230.bed...
plink is available for both Linux ana Windows OS. However the question was for convertf.
So convertf is Linux only. There are also other tools to convert from one format to another, but convertf is the easiest ways.
The only way to do it is from Linux , I don't think think there is Windows version, at least I don't use it.
I use Ubuntu VM for the conversion. The command is
convertf -p parameters_file
In parameters_file you specify the filenames that should be converted and the output file names.
In...
I checked who is the most similar to Etruscans and I compared with some new samples from KapitanAndreevo from the latest dataset.
I can say these are almost between the Etruscans.
Here is the list of the individuals to verify:
TAQ001
TAQ024
TAQ017
TAQ005
TAQ015
TAQ018...
The easiest way - you take a screenshot or save the results as png or pdf file.
However you may save it in another file - for example text file. I created my own scripts to save such data. I can share, but it's not perfect. It just work for me.
To save:
# Find the best result
min_score <-...
Actually: it is the Pop3 in the focus. We test if Pop3 is in the middle between pop1/pop2 or how far is pop3 on one side or another.
This is good to know:
F3(A,B,C) = F4(A,B, A,C)
https://uqrmaie1.github.io/admixtools/reference/qp3pop.html
In the description of the function they generaly...
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