A package for haplotype reconstruction in connected polyploid F1 populations
See PolyOriginCmd for running PolyOrigin in command line interface
See PolyOriginR for running PolyOrigin in R
- Apply to connected F1 in tetraploid (TODO for higher ploidy levels. Limited tests for diploids.)
- Apply to SNP array and GBS data
- Robust to dosage errors in SNP array data
- Robust to dosage uncertainties in low read depth GBS data
- Robust to errors in input genetic or physical map
From the julia (>=v1.6.7, 64-bit) REPL mode, run
julia>]add https://github.com/chaozhi/PolyOrigin.jl
where ] enters Pkg REPL mode.
To update the package, run
julia>]up PolyOrigin
Haplotype reconstruction in a simulated tetraploid population from SNP array data
Haplotype reconstruction in a simulated tetraploid population from GBS data
Haplotype reconstruction in a real 3x3 half-diallel potato population
From the julia REPL mode, run
julia>using PolyOrigin
List the names (types, functions, etc) exported by the package
julia>names(PolyOrigin)
To get help on a name, type ? and the name, e.g. polyOrigin
julia>?polyOrigin
| Output file | Description |
|---|---|
outstem.log |
log file |
outstem_maprefined.csv |
same as input genofile except that marker map being refined |
outstem_parentphased.csv |
same as input genofile except that parents being phased |
outstem_parentphased_corrected.csv |
exported if there exist detected parental errors |
outstem_polyancestry.csv |
genoprob and others (e.g. valent configurations) |
outstem_genoprob.csv |
posterior genotype probabilities for all offspring |
outstem_postdoseprob.csv |
posterior dosage probabilities for all offspring |
outstem_plots |
a folder contains plots of condprob for all offspring if isplot = true |
julia> polyOrigin("geno.csv","ped.csv")
If you use PolyOrigin in your analyses and publish your results, please cite the article:
*Zheng C, Amadeu RR, Munoz PR, and Endelman JB. 2021. Haplotype reconstruction in connected tetraploid F1 populations. https://doi.org/10.1093/genetics/iyab106