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  • consensus from mpileup

    Hi,

    I am trying to call the consensus sequence from an mpileup file using samtools (specifically the vcf2fq command).

    The consensus fastq file is produced, and looks correct, but during the running of vcf2fast I receive the following error(?) numerous times:


    Argument "MRSA252^I2001121^I.^IA^I.^I28.2^I.^IDP=1;;CI95=1.5,0;FQ=..." isn't numeric in numeric lt (<) at /samtools-0.1.16/bcftools/vcfutils.pl line 503, <> line 1958656.

    Could anyone explain to me what this means, and whether I am doing something wrong?!

    Cheers

    Paul

  • #2
    I don't think anything is wrong. It does that at every point where the DP is 1 or 0. The software will fill in N's at those points. Just let it finish, the look at it, it should be alright.

    Comment


    • #3
      Thank you!

      Comment


      • #4
        Thank you!!

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