I am using chimeric reads for my analyses, I am asking some questions in a row these days so I hope I'm not getting annoying :D
bwa mem generates a sam output, it can include supplementary alignments (distinguished by the flag 2048). If I sum up the alignment length of the main alignment and of the supplementary alignment of each read that has one, sometimes I find that it goes beyond the read length.
I would like
bwa mem to search for a supplementary alignment only with the unmapped portion of a read: is this possible?