diff --git a/gwaspy/phasing/phase.py b/gwaspy/phasing/phase.py index f43dbfc..e386f35 100644 --- a/gwaspy/phasing/phase.py +++ b/gwaspy/phasing/phase.py @@ -56,6 +56,7 @@ def main(): parser.add_argument('--pedigree', type=str, default=None) parser.add_argument('--local', action='store_true') parser.add_argument('--billing-project', required=True) + parser.add_argument('--data-type', type=str, default='array', choices=['array', 'wgs']) parser.add_argument('--software', type=str, default='shapeit', choices=['beagle', 'shapeit']) parser.add_argument('--output-filename', type=str, required=True) parser.add_argument('--out-dir', type=str, required=True) @@ -72,6 +73,7 @@ def main(): input_vcf=args.input_vcf, vcf_ref=args.vcf_ref, fam_file=args.pedigree, + data_type=args.data_type, software=args.software, output_filename=args.output_filename, out_dir=args.out_dir)