The PLINK BED, BIM, and FAM Files

The PLINK bed, bim, and fam files are the three mandatory files to run FamPipe. The format of the files can be found in the "PLINK user manual".

The bed file is a binary file containing the genotype information. The bim file contains the SNP names and map positions. Chromosome number, SNP names (i.e., rs ID), and physical positions based on hg19 should be specified. Note that for SNPs with rsID, the rsID should be specified as their SNP names. For SNPs with no rsID, their SNP names should be specified as “chrom:position”. For example, 1:10000 for a SNP at 10000 bp on chromosome 1. The fam file contains the family structure, where the affection status for each individual in the 6th column should be specified. If your have both GWAS and NGS data, they should be merged into a single set of the bed, bim, and fam files before running FamPipe.

Command line options:
  • Read the BED file
    --BED file_name
    Example:
    --BED example/fampipe.bed
  • Read the BIM file
    --BIM file_name
    Example:
    --BIM example/fampipe.bim
  • Read the FAM file
    --FAM file_name
    Example:
    --BED example/fampipe.fam