Update Genetic Positions

Programs such as Merlin, MORGAN and GIGI use the Haldane’s map functions for the genetic positions. By default, FamPipe reads the genetic positions from the third column in the bim file. The positions can also be updated based on the Rutger’s Map.
The values in the third column (genetic positions) in the bim file will be updated using this function. Genetic positions for variants not on Rutgers Map are linearly interpolated based on their physical distances. The latest version of Rutger’s Map can be downloaded from http://compgen.rutgers.edu/download_maps.shtml. The map file for each chromosome should be named as “Rutger_Map_chrX.txt”, where X is the chromosome number. Also please make sure the path for --rutger_folder in the external program path file points to the folder where the map files are placed.

Note:
  1. If you use this function, there must be more than one SNP in the bim file that have identical names in Rutger’s Map.
  2. If you use your own genetic positions in the bim file, please follow the rules for the bim file: - The genetic positions in the third column cannot be duplicated - Every value of the genetic position must be less than 500.
Command line options:
--Rutger_Map
Output:
An updated map (new_XXX.bim) will be saved in the output file folder.