PLINK Error: Too many distinct nonstandard chromosome/contig names.
1
1
Entering edit mode
8 days ago
Michal Nevo ▴ 20

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: all_fish.vcf

PLINK • 114 views
ADD COMMENT
0
Entering edit mode
8 days ago
  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.

ADD COMMENT

Login before adding your answer.

Traffic: 2280 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6