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  • Samtools output more easy??

    Hi!
    I'm using samtools and maq to find SNP in illumina files.
    From MAQ, i have a file .snp (by maq cns2snp) very comprehensible, with a columns that represents the position, 1st-2nd and 3rd calls, the Phred qualities etc...
    By samtools I generated a pileup file and a snp file (from samtools.pl varFilter) that is, for me, more complicated and more difficult to manage by a script perl! Could you know some method to convert these samtools files in an output more easy?

    Thanx!
    Bye bye,
    ME

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