3.1.5 Modify .map File
The .map file contains the information on SNPs. This tab-separated
file is composed of four columns: chromosome identifier, SNP
identifier, position in morgans or centimorgans (our data has the
dummy input 0), and base-pair position (see Note 3). The
pre-modification .map file has the format shown in Table 1a. The
values in second column labeled “SNP identifier” are all missing,
because there is a unique identifier for each SNP in humans but not
in Arabidopsis. We will give identifiers to each SNP by combining
the chromosome identifier and the base-pair position.
1. The .map file we are working on is “1001genomes_snps_only_ACGTN.ped.” Copy this file to a backup file by typing the
following command in the terminal to save your original
data file.
$cp 1001genomes_snps_maf0.1_ACGTN.map 1001genomes_snps_maf0.1_ACGTN.map.b
2. Run the following R script to insert your SNP identifier in the
second column.
Table 1
Formats of .map files with SNP identifiers
(A) The initial .map file format. It is composed of four columns: chromosome,
SNP identifier, position in morgans or centimorgans, and position in bases.
The SNP identifier is missing
1
–
0
8 3
1
–
0
9 2
1
–
0
9 9
1
–
0
1 6 2
1
–
0
1 7 1
(B) Modified .map file with SNP identifier
1
1_83
0
83
1
1_92
0
92
1
1_99
0
99
1
1_162
0
162
1
1_171
0
171
192
Tak Lee and Insuk Lee