If you use/adapt any of these scripts please cite the associated paper: http://www.g3journal.org/content/8/12/3745.abstract
and this repository:
#All scripts are numbered with output/intermediate files included
#Large files required: i.e. VCF file, lepmap .linkage input file will be uploaded to a data repository #as part of the paper submission process
#the files are split into two sets. The first, up to the production of the VCF file containings:
#this includes all commands run for the processing of raw RAD data, production of the denovo parental reference and genotype calling
#and the second for everything following VCF file production i.e. lepmap input preparation, lep map commands and analysis of output
#this includes scripts to filter the genotypes in the VCF file by missing data and segregation types in R
#this is an ipython notebook/jupyter notebook file to join the sex-info file made by hand and the genotype file and to encode genotypes as required by lepmap
#this contains all bash/command line scripts used to carry out linkage mapping with lepmap3
#this is an R script to analyse sex averaged and sex specific maps from lepmap3 mapping #it also includes all scripts to carry out synteny analysis and plot circlize figure 2 and boxplot figure 3