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
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written
by
dorothy.yi.ling •
1 answer
"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?
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