README.md

Polymap workflow

As the workflow showed that after you calling Variantion and got the VCF file, then you just can using the vcf2dosage.pl (only for tetraploid species) or R package like PolyRAD and Updog to get the dosages matrix, and the last to use the polymapR to construct the genetic mapping. Well, also this pipeline will get the locus mapping file for QTLanalysis.

Purpose

So this pipeline was built to analysis polyploid species genetic mapping. Mostly used the polymapR to create the linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents . So, currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. The details of Methods, please see the paper.

Installation

polymapR

polymapR is available on CRAN at polymapR. As with other packages on CRAN, it can be installed directly from within R using the command:

> install.packages("polymapR")

polyRAD

PolyRAD depends on some Bioconductor packages. Before attempting to install polyRAD, YOU should run :

if (!requireNamespace("BiocManager", quietly = TRUE)){
  install.packages("BiocManager")
}
BiocManager::install("pcaMethods")

and You also should install VariantAnnotation R package for import from VCF, and run:

BiocManager::install("VariantAnnotation")

and then install polyRAD from CRAN with :

install.packages("polyRAD")

Updog

Updog provides a suite of methods for genotyping polyploids from next-generation sequencing (NGS) data. You can install updog from CRAN in the usual way:

install.packages("updog")

or install for the current version from github with :

# install.packages("devtools")
devtools::install_github("dcgerard/updog")

Others R packages

install.packages("RColorBrewer")
install.packages("qtl") # https://github.com/kbroman/qtl
install.packages("ASMap") #https://cran.r-project.org/web/packages/ASMap/index.html
install.packages("getopt") # https://cran.r-project.org/web/packages/getopt/index.html

Note : Pipeline was running in Linux environment

Some of My Rosa chinensis project genetic mapping results

• Marker segregation summary

• Plotting a map

• Collinearity

Contact

If you are interested in this pipeline or using, and met any bug, please feel free to Contact me