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How IUPAC ambiguity codes are represented in Burrows-Wheeler transform ?

I am reading about Burrows-Wheeler transform and some tools which have adopted it like BWA and HISAT

and I couldn't figure out how different IUPAC ambiguity codes are represented in Burrows-Wheeler transform !

I highly appreciate if u guys can direct me to any articles dealing with this problem :))

alignment indexing
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updated by lakhujanivijay lakhujanivijay • written by Fadel • Fadel

1 answer

I don't know about BWA but Bowtie 2 considers all ambiguous characters in the reference (including IUPAC nucleotide codes) to be Ns. Since, both uses BWT, the same might be true for BWA.

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written by lakhujanivijay lakhujanivijay

Thanks @Vijay Lakhujani

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written by Fadel • Fadel

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