Comparision of two VCF file with vcftools. Chromosome order error message

Question

[cmonat]

Hi,

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?

Thank you

C.

[Pierre Lindenbaum]

show us the output of:

grep -v "#" Sample_All.vcf | cut -f 1 | uniq | tr "\n" " "

and

grep -v "#" Sample_indA.vcf | cut -f 1 | uniq | tr "\n" " "

Answer 1

[cmonat]

Hi,

I assume the output of these two commands should be the same, right? I have tried to sort my files, and now it seems to work.

Many thanks!

C.