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  • sarbashis
    Member
    • Jun 2010
    • 17
    #1

    Help needed to generate Consensus from alignment

    Dear all,
    I have ngs data of bacterial genome. I have aligned with BWA and using samtools I generated consensus. But consensus contains lots of W,Y, M,K etc. As bacterial genome is haploid how to get rid of this. Could any one tell me region of this heterogeneity. Is it possible to generate consensus with only A,T,G,C only? Thank in advance
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