make BED file from existing BIM and FAM files

Question

[josephine.henry]

Hello everyone,

I have a set on .bim and .fam files by chr and I would like to create the corresponding .bed files. I tried using plink but they require .map or .pgen files as input and I don't have those.

Would you have any ideas on how I can do that ?

Thank you very much for your response

[Nicolas Rosewick]

• bim contains snp information (chr, pos, ref/alt allele)
• fam contains sample information (ID, gender)
• bed contains genetic data for SNP (listed in the bim file) and samples (listed in .fam file)
  Thus it's impossible to regenerate a bed file from only bim and fam

Answer 1

[chrchang523]

Unless you are trying to generate RANDOM genomic data, in which case you should explicitly state that in your question, this question makes no sense. See Nicolas Rosewick’s comment.