INNER CODE UNIT · Python

main

aquaskyline/Clairvoyante · clairvoyante/callVar.py:219

def main():
    parser = argparse.ArgumentParser(
            description="Call variants using a trained Clairvoyante model and tensors of candididate variants" )

    parser.add_argument('--tensor_fn', type=str, default = "PIPE",
            help="Tensor input, use PIPE for standard input")

    parser.add_argument('--chkpnt_fn', type=str, default = None,
            help="Input a checkpoint for testing or continue training")

    parser.add_argument('--call_fn', type=str, default = None,
            help="Output variant predictions")

    parser.add_argument('--qual', type=int, default = None,
            help="If set, variant with equal or higher quality will be marked PASS, or LowQual otherwise, optional")

    parser.add_argument('--sampleName', type=str, default = "SAMPLE",
            help="Define the sample name to be shown in the VCF file")

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