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  • what is the meaning of vcf-stats output for shared snps??

    this was answered . . .

    One of the output files of vcf-stats tool, (*.shared), seems to indicate it counts only only sites where the samples of interest share a non-reference allele. Is this true?? If so, is there a way to find the TOTAL shared alleles (reference or non-reference allele) using this tool?
    out.shared :
    #Shared SNPs Frequency
    0 1383802
    1 574506
    2 495679
    Last edited by BGould; 01-07-2014, 07:55 AM. Reason: answered

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