Error .bim file has a split chromosome. Use --make-bed by itself to remedy this.

[Yunlong Nie]

Hi guys, I got this error with my binary input files with the lastest version 1.9, which seems okay with plink 1.07. 

The error message says "Error .bim file has a split chromosome.  Use --make-bed by itself to remedy this." . Quite confused what this means. 

Any help is appreciated. 

Thanks,

BTW, I am trying to run a pca analysis with plink 1.9. And the input file only contains no sex chromosomes. 

[Christopher Chang]

This means that the .bim file is not sorted by chromosome; you might have some chromosome 5 markers, followed by some chromosome 6 markers, followed by yet more chromosome 5 markers.  Many PLINK 1.9 commands have a problem with this.

If you run "plink --bfile [old name] --make-bed --out [new name]", the new fileset will be sorted by chromosome, and you can proceed with your analysis.

[Yunlong Nie]

Thanks. It works well now. 

[zillur rahman]

Hi,

I am having same problem. 

PLINK v1.90b5.4 64-bit (10 Apr 2018)           www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to 64s_sorted.log.
Options in effect:
  --chr-set 31
  --geno 0.999
  --make-bed
  --out 64s_sorted
  --recode 12
  --vcf 64s.sorted.vcf

177045 MB RAM detected; reserving 88522 MB for main workspace.
--vcf: 64s_sorted-temporary.bed + 64s_sorted-temporary.bim +
64s_sorted-temporary.fam written.

Error: .bim file has a split chromosome.  Use --make-bed by itself to
remedy this.

No matter how I run the command, with or without --geno options.

I have sorted my vcf using picard

picard -Xmx141g SortVcf INPUT=64s.vcf OUTPUT=64s.sorted.vcf

Any help?

Thanks in advance.

Best Regards

Zillur