@@ -56,19 +56,21 @@ In a terminal, execute the following lines:
Input
======
* A reference panel (1000 genome format). The user is expected to provide a reference panel in tsv format with the following columns in that order, without header:
+-----+-----+------------+-----+-----+---------+
| chr | pos | snp_id | ref | alt | MAF |
+=====+=====+============+=====+=====+=========+
| 1 |13116| rs62635286 | T | G |0.0970447|
+-----+-----+------------+-----+-----+---------+
| 1 |13118| rs200579949| A | G |0.0970447|
+-----+-----+------------+-----+-----+---------+
| 1 |14604| rs541940975| A | G | 0.147564|
+-----+-----+------------+-----+-----+---------+
| 1 |14930| rs75454623 | A | G | 0.482228|
+-----+-----+------------+-----+-----+---------+
* A reference panel (1000 genome format). The user is expected to provide a reference panel
in tsv format with the following columns in the following order, without header:
parser.add_argument('--output-folder-1-file',required=False,help="optional location to store the preprocessing in one tabular file with one chromosome columns (useful to compute LDSC correlation for instance)")
parser.add_argument('--percent-sample-size',required=False,help="the proportion (between 0 and 1) of the 90th percentile of the sample size used to filter the SNPs",default=0.7)
parser.add_argument('--minimum-MAF',required=False,help="Filter the reference panel by minimum allele frequency",default=0.01)
parser.add_argument('--mask-MHC',required=False,help="Whether the MHC region should be masked or not. default is False",default=False)
parser.add_argument('--additional-masked-region',required=False,help="List of dictionary containing coordinate of region to mask. For example :[{'chr':6, 'start':50000000, 'end': 70000000}, {'chr':6, 'start':100000000, 'end': 120000000}]",default=None)
parser.add_argument('--minimum-MAF',required=False,help="Filter the reference panel by minimum allele frequency",default='0.01')
parser.add_argument('--mask-MHC',required=False,help="Whether the MHC region should be masked or not. default is False",default='False')
parser.add_argument('--additional-masked-region',required=False,help="List of dictionary containing coordinate of region to mask. For example :[{'chr':6, 'start':50000000, 'end': 70000000}, {'chr':6, 'start':100000000, 'end': 120000000}]",default='None')
parser.add_argument('--imputation-quality-treshold',required=False,help="minimum imputation quality in summary statistics",default=None)
parser.add_argument('--imputation-quality-treshold',required=False,help="minimum imputation quality in summary statistics",default='None')