plink2 fails to calculate allele frequency

Question

[yoser4]

Hello everyone. I am trying to calculate the equal frequency in groups. code show as below:

plink2 --vcf <VCF path> --freq --pheno <population-file path> --loop-cats population

But I now get an error:

r + plink2-temporary.psam written. 99 samples (0 females, 0 males, 99 ambiguous; 99 founders) loaded from plink2-temporary.psam. Error: plink2-temporary.pvar has a split chromosome. Use --make-pgen + --sort-vars to remedy this.

I tried adding at the end of my code:

plink2 --vcf <VCF path> --freq --pheno <population-file path> --make-pgen --sort-vars

But still the same error occurs. I don't know how to fix this, hope someone can help me take a look, thanks a lot

Answer 1

[chrchang523]

Remove —freq from your command. Wait until —make-pgen + —sort-vars has completed, and then run —freq on the resulting sorted .pgen fileset rather than the unsorted VCF.

[yoser4]

thank you very much for your help