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Hi, I was trying to follow the demo and train the model from scratch for 1000G data ( after subsetting 1000 samples) and I get the following error:
```
Launching in training mode...
Reading vcf f…
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Repeat the analysis done in https://www.nature.com/articles/s41598-021-82673-8#Sec2 . In particular, steps 1 and 3 of the phylogenetic analysis are connected.
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Is this the best mode for genetic distance? @stevenweaver @spond
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Dear Dr. Pope,
My name is Jeronymo Dalapicolla, a postdoc at the Instituto Tecnólogico Vale in Belém, Brazil. We have a question about a specific warning that we're getting when we try to run the r…
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Dear Szpiech
Hello,I encountered some issues when using selscan to calculate XP-EHH。
①I don't quite understand the map file.My map file is generated like this：vcftools --vcf SNP_merge.vcf --plin…
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We have to think about basic principles of functions.
1. Less functions is better --> remove aliases, combine similar functions
2. Utilize capabilities of `TreeSE` more --> return `TreeSE` if poss…
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Hello Armando
I ran GONe with five groups, three samples per each group (19 chr).
CHMM : ~3 M SNPs
KY : ~ 9 M SNPs
Mid-south : ~ 11 M SNPs
Southernmost : ~11 M SNPs
Western : ~ 8 M SNPs
I…
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Hi,
Can we use tspOrder2 to order a denovo map? For example, all markers produced from stacks (https://catchenlab.life.illinois.edu/stacks/) results.
Best,
Kun
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## By marker type:
- [ ] SNP
- [ ] Sequence
- [ ] Microsatellite
Please refer to the issue number when making a pull request.
## Questions to address:
- What individual based distances exist?
- What …
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Dear Armando /or GONe team,
I have GONe running smoothly on my data, thanks to you Armando.
I, however, have a few questions regarding the output. Especially, the no. of monomorphic sites (SNPs)…