Comments (3)
The admixtools methods don't use any information that is in VCF files but not in plink files. So even if you wouldn't explicitly convert VCF to plink, any information other than the 0/1/2 genotype calls would be discarded anyway if admixtools read VCFs directly. Allele polarization also doesn't matter for admixtools.
If you have VCF files and don't want to use any of that extra information to filter SNPs or genotypes, then you can just use plink or something similar to do the conversion.
If you do want to use that extra information in some way, then that's a task which is outside the scope of what admixtools does.
from admixtools.
No worries, glad you like it!
I'm not sure which issues you are thinking of in going from VCF to plink or eigenstrat formats, but I assume they have to do with the fact that there is not an unambiguous way to convert VCF to plink, with many edge cases that could be handled in several different ways. I doubt that I could implement this conversion any better than existing programs. So I think the best solution would be to use plink or a similar program to convert VCF to plink.
from admixtools.
Hi Robert,
Many thanks for your quick response. There are a number of issues associated with the conversation from VCF to plink and vice-versa. First of all, there's a huge information loss of all non-genotype data that the user might want to come back to. Also, there are a number of documented issues related to allele polarisation in plink, and datasets merging to list a few.
To read in a vcf, external libraries such as vcfR or PopGenome can be used.
from admixtools.
Related Issues (20)
- est_to_boo does not preserve the SNP block names (number of SNPs), but est_to_loo() does. Is that intended? HOT 2
- large difference of f3 result between admixtools and admixtools2 HOT 1
- Zero drift edges HOT 2
- Behavior affected by other R packages? HOT 2
- Error in if (gimp > 0 && gimp%%plusminus_generations == 0) { : missing value where TRUE/FALSE needed HOT 2
- please add tags/releases HOT 2
- Inconsistent bootstrap significance testing HOT 5
- keyword argument typo lack of error HOT 3
- Comparing graphs with compare_fits HOT 2
- auto_only: change default value to FALSE HOT 1
- qpWave returning one fewer ranks than expected HOT 1
- qpAdm computation stucks when the num. of letf pops below 3
- Issue with f3 and f4 HOT 2
- running many replicates of find_graphs? HOT 1
- Issue with extract_f2 HOT 2
- Problem making f2 file from plink .bed .fam and .bim files HOT 6
- Suggestion: Change to p_emp calculation in compare_fits() HOT 1
- possible to get worst residuals from `find_graphs` models? HOT 1
- Installation / Update error HOT 4
- Interpretation of qpadm results
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from admixtools.