I'm using the vcftools for the first time. I'm trying to compare two VCF files with the following command line:
vcftools --vcf Sample_All.vcf --diff Sample_indA.vcf --diff-site --out Multiple_vs_indA
and I get the following error message:
Error: Both files must be sorted in the same chromosomal order.
chr1 in file 2 appears to be out of order.
But I know that in both VCF file I have the chr1 included, so, why do I have this message?
Plus I have tried to had the "--not-chr chr1" parameter to my command line, as I understand it was advised to do in this case, but then I have the same error message but on chr2 ...
Is it normal? What should I do to resolve this issue? Or maybe it is just a warning message?