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Use plink2treemix.py to convert the file format, the rest should hopefully be straightforward.
```
Added a small script to convert stratified allele frequencies output from plink into TreeMix for…
na399 updated
7 years ago
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I see this question. could you answer please?
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Hi, apologies if this is not the right way to get in touch regarding this issue.
I have attempted to do this command:
`
treemix -i data.p.treemix.gz -o output
`
And this results in the err…
hemr3 updated
2 weeks ago
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Hi!
I got a strange Error reported. It showed that a the title. However, I produced `f2-summary statistics` by the instruction Step 1, which was normal and no any error repoted, but the Step 2 runnin…
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9 hours ago
[reza](https://www.biostars.org/u/29720/) ▴ 300
I run treemix with bootstraping using Treemix_bootstrap.sh (BITE R package) with one migration event. it worked without any error. Now w…
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Hello,
I am trying to convert a vcf file to a treemix input file using the vcf_to_treemix.py script and I keep getting the following error regarding the json decoder:
` json.decoder.JSONDecodeErr…
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Hello,
I am running the Step3_TreeMix.sh with m=4. I use this code:
sh Step3_TreeMix.sh nomissing.populations.treemix.gz 6 1 noRoot 300 4 m4 100 Step1_out/nomissing.4_outtree.newick /home/yeser…
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https://github.com/QuentinRougemont/treemix_workflow/blob/975ba9997dc55ed8e3308b05749706712a662124/01.scripts/utility_scripts/00.vcf_to_treemix.sh#L5
Hello, I am trying to use this to convert vcf t…
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Hi
I Need Convert plink(bed-bim-fam) to treemix input
With This Command:
glactools bplink2acf --fai human_g1k_v37.fasta.fai afghan | glactools acf2treemix - | gzip > treemix.gz
but error:
Can…
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Hi,
I ran this:
`python vcf2treemix.py -vcf file.vcf -pop poplist.txt`
I got one output: "file.tmix"
```
head file.tmix
A B C D E F G
24,11 27,13 12,9 16,10 22,8 22,13 21,8
27,14 36,10 2…