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Old 02-10-2017, 07:27 AM   #1
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Location: Germany

Join Date: Nov 2015
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Default Comparing two VCF files with vcftools, chromosome out ouf order error message


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
cmonat is offline   Reply With Quote
Old 02-14-2017, 08:57 PM   #2
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
finswimmer is offline   Reply With Quote

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