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Old 01-20-2012, 04:00 AM   #1
Location: Pittsburgh

Join Date: Aug 2011
Posts: 72
Default sorting vcf- can't get vcftools to work

I am trying to run CountCovariates in GATK. I downloaded the most recent dbsnp file from the broad institute site. The problem is it is not sorted in chromosomal order. I have vcf-tools installed and tried to sort using the -c command. It is telling me "Obsolete version of sort command installed, please run without the -c option." But, if I type in vcf-sort -h , the usage says the -c is available. I have checked to make sure we have the most recent version. I don't find the vcf-tools website to be very helpful. Could someone point me in the right direction or do you know where I can download a sorted vcf file? Is there another program that I can use?
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Old 01-20-2012, 04:46 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

I'm not sure which version of vcf-tools you have. The most recent one (0.1.7) doesn't have a -c option for vcf-sort. Perhaps try updating vcf-tools.
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Old 01-25-2012, 05:18 AM   #3
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Location: Europe

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The -c works only on system with newer unix sort commands which support the --version-sort option.
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