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  • Vcftools to convert vcf to plink, help

    I have been trying to use vcftools to convert a vcf file into plink ped and map files.

    If I separate my vcf by chromosome, then the it works. If I leave it as a whole file, it appears to run fine, but when I use the converted files with plink, I receive the following error:

    ERROR:
    A problem with line 1 in [ 25215.ped ]
    Expecting 6 + 2 * 87492462 = 174984930 columns, but found 104052725


    Any idea why this is, or how to fix it?
    Thanks!

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