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, 13:16, 14 April 2014
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| * If --kinxFile is not used, but --kinFile your.autosomal.Empirical.Kinship.gz --vcX are issued in a command line, then RAREMETALWORKER will look for a kinship X file named your.autosomal.Empirical.KinshipX.gz. If this file is still not found, a FATAL ERROR will occur. | | * If --kinxFile is not used, but --kinFile your.autosomal.Empirical.Kinship.gz --vcX are issued in a command line, then RAREMETALWORKER will look for a kinship X file named your.autosomal.Empirical.KinshipX.gz. If this file is still not found, a FATAL ERROR will occur. |
| ===--kinSave=== | | ===--kinSave=== |
| + | * This option must be used with --kinGeno. |
| + | * Issuing --kinSave will request [[RAREMETALWORKER]] to store the estimated GMR in a file named yourprefix.Empirical.Kinship.gz. |
| + | * If --vcX is also issued in the command line, then a separate file named yourprefix.Empirical.KinshipX.gz will be generated where the GRM of chromosome X is saved. |
| *For formats of the saved genomic relationship matrix, please refer to [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']]. | | *For formats of the saved genomic relationship matrix, please refer to [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']]. |
| + | |
| ==Kinship Options== | | ==Kinship Options== |
| ===--kinMaf=== | | ===--kinMaf=== |