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  • Mr Mutundes
    Member
    • Jan 2009
    • 17
    #1

    bwa - samtools - SNPs

    Hi,

    I am interested in hearing from anyone who has successfully used the combination of bwa and samtools to identify SNPs from paired SOLiD reads. Working with simulated reads at the moment I am getting nice alignments but my pileup output from samtools is pretty wacky... so I'd like to know if in anyone else's hands this can actually work.

    Thanks
    Tags: None
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