pon_creation.py

from paths import GetPaths


class PonCreation(object):
    def __init__(self, normal_file, normal_target_interval):
        self.get_paths = GetPaths()
        self.normal_bam = normal_file
        self.normal_interval = normal_target_interval
        self.output_vcf = "output." + str(self.normal_bam).split("/")


    def create_normal_for_pon(self):
        command = "java -jar + " + self.get_paths.gatk_path + " -T HaplotypeCaller -R " + self.get_paths.ref_dir + \
                  "reference.fasta -I:" + self.normal_bam + " [--dbsnp " + self.get_paths.dbsnp + "] [--cosmic " + \
        self.get_paths.cosmic + "] --artifact_detection_mode [-L " + self.normal_interval + "] -o output.normal1.vcf"

    def combine_pon(self):
        command=" java -jar GenomeAnalysisTK.jar T CombineVariants -R reference.fasta " \
                "-V output.normal1.vcf -V output.normal2.vcf [-V output.normal2.vcf ...] -minN 2 --setKey \"null\" " \
                "--filteredAreUncalled --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED [-L targets.interval_list] " \
                "-o MuTect2_PON.vcf"