PCA: Invalid chr code when using --chr-set and --allow-extra-chr

[nag...@oregonstate.edu]

I'm having difficulty getting PLINK to calculate PCAs for a tped/tfam from a nonmodel species. I'd tried many times now and don't know what else to do differently, and would really appreciate some pointers. This is similar to problems others have had in this group, but the solutions aren't working for me.

Full Command: plink --tfile all_emmax_format_12 --pca 5 --allow-extra-chr --chr-set 19 

Error: Invalid chromosome code '96' on line 7728294 of .tped file.

(This is disallowed by your --chr-set/--autosome-num parameters.  Check if the

problem is with your data, or your command line.)

I think --chr-set is supposed to be the number of autosomes (19 for my nonmodel species) but I've tried it with 3664 (number of total scaffolds including unassembled contigs) as well and understand --chr-set can't take a number that high. Is this correct?

My understanding is that I have to use --allow-extra-chr in this case.

The input tped and tfam look as they should. These files came from PLINK and I know the files are okay because I used them for EMMAX, which stops if there's any formatting issue.

Is it not possible to calculate covariates using PLINK when there are so many scaffolds? Is that the problem?

Thanks,

Michael Nagle

PhD student, Molecular and Cellular Biology

[Christopher Chang]

Scaffold names can’t be numeric. Change them to scaffold1, scaffold2, etc. and you should be fine.

[Luis Cueto]

Hi Christopher,

I am trapped in a loop. I have to add letters to the chromosomes' names to create the .ped file, but when I try to use that .ped file to run Admixture, I am asked to use only integers in the chromosome names.
I am working with 1265 scaffolds.
Any recommendation? 

[Christopher Chang]

0. You should prefer .bed+.bim+.fam to .ped+.map >99% of the time in 2023.  .ped+.map loses minor allele codes and is also far less efficient in both space and time.

1. Right before handing off the data to Admixture, you can use "--allow-extra-chr 0" to convert all the scaffold codes to "0", which Admixture should accept.

[Luis Cueto]

Thanks for your prompt reply!

It worked!