Plink1.9 error -chr not recognised

Question

[giulia.trauzzi]

Hello, I am trying to run PLink on my tped file (SNP data set) to test for linkage disequilibrium, but it appears as if I need to set some chromosome options because I get some error at some line.

My data is not mapped.

this is the error I get.

Error: Invalid chromosome code '27' on line 12 of .tped 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.)

This is my line of code

plink --tped paua_snps_plink.tped --indep-pairwise 50 5 0.5 --allow-extra-chr --out paua_snps_plink_out --tfam paua_snps_plink.tfam

I have tried to change the option with --allow-extra-chr 0 but I still get the same message... I am trying to run the same line with Plink2, maybe it is a bug?

I am not sure what I am doing wrong. I have googled it but I don't know how to fix this. Do I need mapped data to use plink to test for LD in a SNP data set?

Cheers,

Giulia

[strive]

Hi, Have you solved your problem? I have also been using plink v1.9 recently and have encountered the same problem, but I don't know how to deal with it, do you want to talk about it?

Thanks

Ling

[giulia.trauzzi]

Hi Ling,

I am sorry I did not solve the issue because I ended up using something else as my data was not mapped against a reference genome. I am suspecting that was the issue. If it can help, I have used the R package genetics and the function LD to test for LD on my unmapped vcf file.

Good luck

Giulia

[strive]

Hi Giulia: I am sorry too late reply you, I used the VCF file and try to append a letter to the #CHROM numbers, the error message disappeared. I hope it can help you.

Good luck ling

Answer 1

[Kevin Blighe]

Hi,

Which species is this? It implies that you have a contig / chromosome ID of '27' in your data, but the default assumption of PLINK's commands is that your data is from human.

As per the error message, you probably just need to set a value for --chr-set with your commands. Please see: https://www.cog-genomics.org/plink/1.9/input#chr_set

Kevin

[giulia.trauzzi]

Hi Kevin,

thanks for your reply.

I am working with abalone, but my data is unmapped. The SNPs were generated via de novo, so the coding below the column CHR has no meaning.

Could I still be using Plink?

Cheers,

Giulia

[Kevin Blighe]

Oh, nice, abalone. To avail of --indep-pairwise 50 5 0.5, I think that you will need positional (mapping) information. Can you share an example portion of the map file?; or share the output of the following command, assuming that there are no data access restrictions with the data:

cut -f1-6 -d" " paua_snps_plink.tped | head

Answer 2

[Kathy]

Yes, You only need to put the number of chromosomes you have in your analysis --chr-set 27 (if it is the maximum number of chromosomes), if you have more you should put the maximum number you have, that will depend on the species:

plink --tped paua_snps_plink.tped --indep-pairwise 50 5 0.5 --chr-set 27 --tfam paua_snps_plink.tfam --out paua_snps_plink_out

---