def run_genotyper(bam_file, ref_file, dbsnp_file, config_file):
    """Perform SNP genotyping and analysis using GATK.
    """
    cl = ["gatk_genotyper.py", config_file, ref_file, bam_file]
    if dbsnp_file:
        cl.append(dbsnp_file)
    subprocess.check_call(cl)
def run_genotyper ( bam_file , ref_file , dbsnp_file , config_file ) : cl = [ "gatk_genotyper.py" , config_file , ref_file , bam_file ] if dbsnp_file : cl . append ( dbsnp_file ) subprocess . check_call ( cl )
Perform SNP genotyping and analysis using GATK.