def extract_germline_vcinfo(data, out_dir):
    """Extract germline VCFs from existing tumor inputs.
    """
    supported_germline = set(["vardict", "octopus", "freebayes"])
    if dd.get_phenotype(data) in ["tumor"]:
        for v in _get_variants(data):
            if v.get("variantcaller") in supported_germline:
                if v.get("germline"):
                    return v
                else:
                    d = utils.deepish_copy(data)
                    d["vrn_file"] = v["vrn_file"]
                    gd = germline.extract(d, [d], out_dir)
                    v["germline"] = gd["vrn_file_plus"]["germline"]
                    return v
def extract_germline_vcinfo ( data , out_dir ) : supported_germline = set ( [ "vardict" , "octopus" , "freebayes" ] ) if dd . get_phenotype ( data ) in [ "tumor" ] : for v in _get_variants ( data ) : if v . get ( "variantcaller" ) in supported_germline : if v . get ( "germline" ) : return v else : d = utils . deepish_copy ( data ) d [ "vrn_file" ] = v [ "vrn_file" ] gd = germline . extract ( d , [ d ] , out_dir ) v [ "germline" ] = gd [ "vrn_file_plus" ] [ "germline" ] return v
Extract germline VCFs from existing tumor inputs.