makeSNPnamesUnique.R

# About -------------------------------------------------------------------
# 10/06/2021
#
# Reference: https://www.biostars.org/p/9474813/
#
# input: BIM filname
# Note: This script will overwrite the existing input bim file
#
# example run: 
# Rscript makeSNPnamesUnique.R myBimFile.bim

# Input arguments ---------------------------------------------------------
args <- commandArgs(trailingOnly = TRUE)
fileBim <- args[1]

# Data --------------------------------------------------------------------
bim <- read.table(fileBim, header = FALSE, stringsAsFactors = FALSE)

# make unique names
bim$V2 <- 
  make.unique(
    ifelse(bim$V2 == ".",
           paste(bim$V1, bim$V4, bim$V5, bim$V6, sep = "_"),
           bim$V2),
    sep = "_")
            
# Output ------------------------------------------------------------------
write.table(bim, file = fileBim,
            col.names = FALSE, row.names = FALSE, quote = FALSE,
            sep = "\t")