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library(dplyr)
library(qqman)
library(readr)
args = commandArgs(trailingOnly=TRUE)
if (length(args) != 1) {
write("Usage: Rscript jwas-manhattan.r GWAS-FILE", stderr())
quit(status=1)
}
gwas_file = args[1]
gwas = mutate(read_tsv(gwas_file), antilog=10^(-modelfrequency))
manhattan(gwas, chr="chromosome", bp="position", snp="marker_ID", p="antilog")
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