PLINK file formats: .bim and .fam

Generate test files

Content of test1.ped:

fabu peter 0 0                                        1  0    G G    2 2    C C
fabu mary 0 0                                         1  0    A A    0 0    A C
fabu jane peter mary                                  1  2    0 0    1 2    A C
awesome davidson 0 0                                  1  0    A A    2 2    0 0
awesome lisalistanovlivasa 0 0                        1  2    A A    2 2    0 0
awesome james-liang davidson lisalistanovlivasa       1  2    A A    2 2    A A

Contentof test1.map:

1 snp1 0 1
1 snp2 0 2
1 snp3 0 3

Generate .bed .bim and .fam files:

plink --file test1 --make-bed --out test1

BIM files

Tab delimited. The fields in a BIM file are:

Chromosome code (either an integer, or 'X'/'Y'/'XY'/'MT'; '0' indicates unknown) or name

Variant identifier

Position in morgans or centimorgans (safe to use dummy value of '0')

Base-pair coordinate (normally 1-based, but 0 ok; limited to 231-2)

Allele 1 (corresponding to clear bits in .bed; usually minor)

Allele 2 (corresponding to set bits in .bed; usually major) 

Content of generated (tab delimited) bim file:

1 snp1 0 1 G A
1 snp2 0 2 1 2
1 snp3 0 3 A C

FAM files

Space delimited. The fields in a FAM file are:

    Family ID
    Sample ID
    Paternal ID
    Maternal ID
    Sex (1=male; 2=female; other=unknown)
    Affection (0=unknown; 1=unaffected; 2=affected)

Content of generated (space delimited) fam file:

fabu peter 0 0 1 -9
fabu mary 0 0 1 -9
fabu jane peter mary 1 2
awesome davidson 0 0 1 -9
awesome lisalistanovlivasa 0 0 1 2
awesome james-liang davidson lisalistanovlivasa 1 2