Bwa : Allow Low Stringency In Alignments

Question

[Nicolas Rosewick]

Hi,

I wonder if it's possible to allow small local alignment using bwa. Per example: with 2x100bp reads, to output all alignment with minimum 10 bases mapped ? So a very loose alignment.

Thanks

[Andreas]

I think you might be better of with a Smith-Waterman implementation like 'bwa bwasw', but am not sure what the smallest possible match is.

Andreas

Answer 1

[Chris Fields]

Maybe have a look at bwa mem (in newer releases of bwa, post 0.7 I believe). It has a mismatch penalty, so you can try playing with that as well as seed length.

lh3's paper on bwa-mem is in arxiv and is also described elsewhere in biostar.