PLINK Binary files (BED/BIM/FAM)

PLINK is a very widely used application for analyzing genotypic data. It can be considered the “de-facto” standard of the field, although newer formats are starting to be widespread as well. The binary PLINK format description can be accessed  at their site

The binary PLINK fromat contains the same information as the flat file PLINK format but in a compressed and signifficantly more efficient form. You may use the FAM file to deliver sex and affection data for GWASpi to perform GWS studies. Optionally, if you want to provide the additional data fields that GWASpi supports, you may chose to use the Sample Info & Phenotype format.

BED files

The BED files are encoded in binary format. A description of it’s content con be found here

BIM files

The fields in a MAP file are:

  • Chromosome
  • Marker ID
  • Genetic distance
  • Physical position
  • Allele 1
  • Allele 2
Example of a BIM file of the binary PLINK format:
21 rs11511647 0 26765 A T
X rs3883674 0 32380 C G
X rs12218882 0 48172 T T
9 rs10904045 0 48426 A T
9 rs10751931 0 49949 C T
8 rs11252127 0 52087 A C
10 rs12775203 0 52277 A A
8 rs12255619 0 52481 G T

FAM files

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)
Example of a FAM file of the binary PLINK format:
FAM1 NA06985 0 0 1 1
FAM1 NA06991 0 0 1 1
0 NA06993 0 0 1 1
0 NA06994 0 0 1 1
0 NA07000 0 0 2 1
0 NA07019 0 0 1 1
0 NA07022 0 0 2 1
0 NA07029 0 0 1 1
FAM2 NA07056 0 0 0 2
FAM2 NA07345 0 0 1 1