PLINK Error: Too many distinct nonstandard chromosome/contig names.

Question

[Michal Nevo]

plink_converter.txt :

--noweb --const-fid 0 --allow-extra-chr 0 --vcf /storage/users/IsanaRNA/FISH_DATA/MappingToAssembeledGenome/files_for_Plink/all_fish_plink.vcf --recode --out myPlinkFile

my command:

plink --script plink_converter.txt

PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to myPlinkFile.log.
Options in effect:
  --allow-extra-chr 0
  --const-fid 0
  --noweb
  --out myPlinkFile
  --recode
  --vcf /storage/users/IsanaRNA/FISH_DATA/MappingToAssembeledGenome/files_for_Plink/all_fish_plink.vcf

Note: --noweb has no effect since no web check is implemented yet.
31993 MB RAM detected; reserving 15996 MB for main workspace.
--vcf: 1338k variants complete.
Error: Too many distinct nonstandard chromosome/contig names.

What can I do?

I have 10 samples I merged into one vcf file all_fish.vcf:

Answer 1

[chrchang523]

1. This script doesn’t really make sense in 2021: VCF is more plink-compatible than the .ped+.map format generated by —recode (which is simultaneously slower, less scalable, and not even valid input at all for plink 2.0). Try to either use —make-bed to convert it to plink 1.9’s native format, or just leave it as a VCF.

2. To get past the immediate issue, you can use a short shell script to replace all the chromosome codes with “0” in the VCF first (and this makes explicit “—allow-extra-chr 0” unnecessary). You will probably want to assign unique position-based variant IDs at the same time.