3 Using MapThin

The program MapThin takes a PLINK map file as input (either .map or .bim) and produces another map file with less SNPs than the original. The SNPs in the map file should be ordered by chromosome and then by genetic distance (cM) (or base pair position if the -b option is used). The SNPs that are kept in the new map file are chosen to be as evenly spaced as possible.

Note: The units for genetic distance in PLINK files is by default morgans (M), whereas MapThin uses centimorgans (cM) and requires genetic distance data to be in cM. The --cm option in PLINK can be used to specify centimorgans.

Basic usage of the program is given by typing:

./mapthin data.map thinned.map

This will thin the map file using the default value of 2.4 SNPs per cM. The number of SNPs to take from the original may be set by setting one of three options: (i) the SNPs per cM, (ii) the absolute number of SNPs to keep, or (iii) The percentage of SNPs to keep. Typing mapthin with no options will output usage details:

MapThin (v1.02): Thinning your map files!
------------------------------------------------------------
Copyright 2012 Richard Howey, GNU General Public License, v3
Institute of Genetic Medicine, Newcastle University

Usage:
         ./mapthin [options] data-in.map data-out.map

Options:
  -t x          -- SNPs per cM, x
  -s y          -- Total no. of SNPs to keep, y
  -p z          -- Percentage of SNPs to keep, z
  -b [w]        -- Use base pair position [with w SNPs per 10^6 bpp in file]
  -n            -- Output the name of the SNPs only
  -so           -- suppress output to screen

Default Options:
  -t 2.4