Comparing two VCF files with vcftools, chromosome out ouf order error message

cmonat · 02-10-2017, 07:27 AM

Hi,

I'm using the vcftools for the first time. I'm trying to compare two VCF files with the following command line:

Code:

vcftools --vcf Sample_All.vcf --diff Sample_indA.vcf --diff-site --out Multiple_vs_indA

and I get the following error message:

Code:

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

Code:

--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.

finswimmer · 02-14-2017, 08:57 PM

Hello cmonat,

take a look inside both vcf files and check whether they are ordered correct by chromosom and position.

fin swimmer

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02-10-2017, 07:27 AM	#1
cmonat Junior Member Location: Germany Join Date: Nov 2015 Posts: 4	Comparing two VCF files with vcftools, chromosome out ouf order error message Hi, I'm using the vcftools for the first time. I'm trying to compare two VCF files with the following command line: Code: vcftools --vcf Sample_All.vcf --diff Sample_indA.vcf --diff-site --out Multiple_vs_indA and I get the following error message: Code: 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 Code: --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.

02-14-2017, 08:57 PM	#2
finswimmer Member Location: Europe Join Date: Oct 2016 Posts: 60	Hello cmonat, take a look inside both vcf files and check whether they are ordered correct by chromosom and position. fin swimmer