Ungapped Alignment In Bwa

Question

[Higherdefender]

Hi,

I am new to the field of bioinformatics. Currently, I am playing with bwa sequence alignment tool. As I read through the manual, I couldn't understand how to do un-gapped alignments in "bwa"(short read one)(default option is gapped). This is a very rookie question and of no use, but I need to do it for comparison purposes and I just can't figure it out. Please help.

Thanks.

P.S. Is it done by setting option -M to 0?

Answer 1

[Docroberson]

I haven't tried to do an ungapped alignment with BWA, but I would think setting "-o 0" would disable gapping by setting the maximum number of gap openings to 0.