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

Question

[Fadel]

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 :))

Answer 1

[lakhujanivijay]

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.

[Fadel]

Thanks @Vijay Lakhujani