Invalid chromosome code

[Courtney Gardiner]

Hi there

I am trying to convert a very large .vcf file to a .bed file using Plink (I have tried both 1.90 and 2) to use in pcadapt down the line. This is the code I have been using:

plink --vcf ./BCFTools_MP/MP_filtered.recode.vcf --allow-extra-chr --double-id --make-bed --out ./BCFTools_MP/MP_filtered.recode

I receive the following error: 

Error: Invalid chromosome code '40' on line 88802 of .vcf file.

(This is disallowed for humans. Check if the problem is with your data, or if you forgot to define a different chromosome set with e.g. --chr-set.)

I thought that by including "--allow-extra-chr" I was circumventing this problem. I am working on a fish species and the reference genome I'm using is highly fragmented and at scaffold level. I have since gone back and added "chr" to each chromosome code but it is still not working. It seems like a fairly simple issue but I can't seem to resolve it. 

[Chris Chang]

—allow-extra-chr allows generic alphabetic chromosome codes (and is no longer necessary in recent plink2 development builds).  —chr-set (

https://www.cog-genomics.org/plink/2.0/input#chr_set ) changes the interpretation of numeric chromosome codes; by default, 23 is chrX, and you don’t want that.

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[Chris Chang]

Forgot to mention, “chr” prefixes are special (they’re treated like no prefix at all), you need to add another prefix like “contig” when dealing with scaffolds.

On Tue, Feb 13, 2024 at 6:35 AM Courtney Gardiner <courtsg...@gmail.com> wrote:

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[Courtney Gardiner]

Hi thank you so much for the reply and apologies for the delay on my end.

As mentioned I have a very fragmented genome at scaffold level with 532902 scaffolds. My VCF file is 2.9 GB so it is extremely large. I don't have any information on the number of chromosomes for my study species to specify with -chr-set. Do I understand correctly that the best way to work around this would be to just add "contig" as a prefix? Or are there other workarounds I should implement? Can you let me know what you think the best course of action would be?

I am now using PLINK 2.0 for this conversion but am still running into problems. 

[Christopher Chang]

Yes, you should add "contig" as a prefix, and then use a PLINK 2.0 build supporting a large number of contigs (see https://groups.google.com/g/plink2-users/c/pWGwFrE_ex0/m/dLpFBVQLAQAJ for a link to a compiled March 2024 build).