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  • luc
    Senior Member
    • Dec 2010
    • 469
    #1

    How do aligners deal with ambiguous bases?

    Hi,

    I would be interested to know how do aligners for HT sequencing data (BBmap, Bowtie, BWA-mem, .. etc.) deal with ambiguous bases?

    Are they able to ignore the position of an N in the sequence alignment or are they substituting a random base?
    Are there any circumstances for which it would be preferable to convert single low quality bases in the middle of the reads into Ns to avoid problems with variant calling?
    Thanks in advance!
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