snplist2ChrPosition_TASSEL.r

# Clear and set up workspace
rm(list = ls())
library(tidyverse)

# set your working directory as appropriate for your computer
#setwd("XXXXXXXXXXXXXXXXXXXXXX")

# ###
# # generate an example list of SNPs for the demonstration
# ###
# # read in the tutorial data
# fullMap <- read_tsv("mdp_genotype.plk.map", col_names = F)
# # generate list of SNPs
# nExample <- 50
# fullMap[sample(1:nrow(fullMap), nExample),2] %>%
#   write_tsv("exampleSnpList.txt", col_names = F)

###
# prepare a bed file from a SNP name list
###
# read in the file with SNP names
snpList <- read_table("exampleSnpList.txt", col_names = F) %>%
  rename(snpName = X1)
# read in the map file with SNP positions (full info)
fullMap <- read_tsv("mdp_genotype.plk.map", col_names = F) %>%
  rename(chromosome = X1, snpName = X2, morgan = X3, position = X4)

# write out a chromosome + position file to be loaded in TASSEL
tmp <- inner_join(snpList, fullMap) %>%
  select(chromosome, position) %>%
  write_tsv(., "SnpName2ChrPosition_TASSEL.txt", col_names = F)