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  • 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?

  • #2
    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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    • #3
      The -c works only on system with newer unix sort commands which support the --version-sort option.

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