snp-pileup-wrapper.R

#!/usr/bin/env Rscript
suppressPackageStartupMessages({
    library(argparse)
})

args = commandArgs(TRUE)
if (length(args) == 0) {
    message('Run snp-pileup-wrapper.R --help for list of input arguments.')
    quit()
}

parser = ArgumentParser(description = 'Generate SNP read counts from matched tumor-normal BAM files.')

parser$add_argument('-v', '--verbose', action = "store_true", default = TRUE,
                    help = 'Print run info')
parser$add_argument('-sp', '--snp-pileup-path', required = FALSE,
                    help = 'Path to snp-pileup executable [default environment variable $SNP_PILEUP]')
parser$add_argument('-vcf', '--vcf-file', required = TRUE,
                    help = 'Path to VCF file containing SNP positions')
parser$add_argument('-n', '--normal-bam', required = TRUE,
                    help = 'Path to normal sample BAM file')
parser$add_argument('-t', '--tumor-bam', required = TRUE,
                    help = 'Path to tumor sample BAM file')
parser$add_argument('-o', '--output-prefix', required = TRUE,
                    help = 'Name prefix for output file')
parser$add_argument('-p', '--pseudo-snps', required = FALSE, default = 50,
                    help = 'Do pileup at every p:th position [default %(default)s]')
parser$add_argument('-d', '--max-depth', required = FALSE, default = 4000,
                    help = 'Maximum read depth [default %(default)s]')

args = parser$parse_args()

# Prepare output --------------------------------------------------------------------------------------------------

snp_pileup_env = Sys.getenv('SNP_PILEUP')

if (is.null(args$snp_pileup_path)) {
    if (snp_pileup_env == '') {
        stop(paste('No snp-pileup path provided or in user environment.'), call. = F)
    } else {
        snp_pileup_path = snp_pileup_env
    }
}


output_file = paste0(args$output_prefix, '.snp_pileup.gz')

if (file.exists(output_file)) {
    stop(paste(output_file, 'already exists. Remove before running.'), call. = F)
}

default_args = c('--count-orphans --gzip')

pileup_cmd = paste(
    snp_pileup_path,
    default_args,
    '-P', args$pseudo_snps,
    '-d', args$max_depth,
    args$vcf_file,
    output_file,
    args$normal_bam,
    args$tumor_bam
    )

system(pileup_cmd)