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  • Find common SNP in vcf files.

    Hi,

    I have vcf files for 6 individuals and I would like to find SNP's that occur in all 6 vcf files. Any ideas how this can be done, I can write a script to do this but if it is been done I don't want to waste time. To note , I dont want to lose what the SNP call for each individuals, so I would like 6 vcf files one for each individual containing only SNP's that are present in the other lines.

    Any help would be appreciated.

  • #2
    See if this would do. VCFtools: http://vcftools.sourceforge.net/

    Usage: http://vcftools.sourceforge.net/man_latest.html
    Last edited by GenoMax; 05-11-2015, 01:20 AM.

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    • #3
      I thanks, I am reading the VCF tools currently and I have used it. Was wondering if anyone has an command example that would achieve this.

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