Manage Deletions - C++

Question

[MarioRio]

Hi, my program analyze mutations in a BAM file after a comparison with the FASTA. The problem comes when an alignment has a base deletion, because the next bases move back in position clinging at the rest of the read. Is there a a function or something else in C++ bamtools library that can automatically extract the deletion information and manage it? If not, how can i resolve it?

thanks in advance

Answer 1

[Pierre Lindenbaum]

You could try to align the sequence of the read with the reference using a Smith-Waterman algorithm.

The second result of https://www.google.com/search?q=Smith+Waterman+filetype%3Acpp is a link to BandedSmithWaterman.cpp

"CBandedSmithWaterman - aligns reads using a banded Smith-Waterman algorithm"

https://code.google.com/p/mosaik-aligner/source/browse/src/CommonSource/PairwiseAlignment/BandedSmithWaterman.cpp