PLINK input files not found (adds .fam to input.bed)

Question

[michael.nagle]

I'm trying to use PLINK to generate a .tped file from a .fam file, to prepare for EMMAX. I'm following instructions for EMMAX from the inventors at UCLA: http://genetics.cs.ucla.edu/emmax/install.html

This states: "1. Use PLINK software to transpose your genotype files (bed or ped format) to tped/tfam format by running % plink --bfile [bed_prefix] (or --file [ped_prefix]) --recode12 --output-missing-genotype 0 --transpose --out [tped_prefix] "

These instructions are unclear. I assume [bed_prefix] and [tped_prefix] are positions to insert the input and output filenames, minus the file extension suffix...?

I've tried with and without the suffixes. Either way, I get the same error.

With prefix only for filenames:

plink --bfile input --recode12 --output-missing-genotype 0 --transpose --out output

Error: No file [ input.fam ] exists.

With whole filenames:

plink --bfile input.bed --recode12 --output-missing-genotype 0 --transpose --out output.tped

Error: No file [ input.bed.fam ] exists.

I can't figure out why I'm getting these errors when I seem to be following the instructions, and am not using any options to tell it to look for a .fam file... No idea where it's getting this from. I'd appreciate help on what may be the problem. Thanks much.

[chrchang523]

What genotype files do you have? Neither .bed nor .ped files make sense on their own; plink .bed files must be accompanied by a .bim and a .fam file, while plink .ped files must be accompanied by a .map.

[michael.nagle]

My genotype files are .bed and I'm trying to use PLINK to convert them to .ped.

[chrchang523]

You need to get your hands on the .bim and .fam that originally accompanied the .bed, then.