Require help in using PLINK flags and scripts

Question

[dorothy.yi.ling]

Hi all,

I am trying to use some PLINK flags --geno and --maf to do some quality control filtering on my SNPs bed files (bed, bim and fam). The flags seemed to have worked fine but I received this error:

Error: Invalid header bytes in .bed file.

I have no idea what it means since I have been using the bed files for a few times and they had no problem.

I hope someone who is using PLINK would know the answer! Many thanks! Doro

Here is my script:

/{directory}/plink --bfile /{directory}/new_baependi/Baependi_release3_filtered_batch1_3_chr22.impute2 --make-bed --geno 0.05 --maf 0.005 --out / {directory}/Baependi_release3_qc_batch1_3_chr22.impute2

[christopher medway]

can you post the first few lines from you bed file

Answer 1

[chrchang523]

"Invalid header bytes in .bed file" means that your --bfile parameter does not actually correspond to a PLINK 1 .bed file. In this case, it looks like you have a genotype fileset from IMPUTE2. Did you previously convert it to .bed+.bim+.fam, but accidentally type ".impute2" at the end here?