flag settings for perfect-matched alignments

[zhenzhenyang-psu]

HI Dr. Li, I want to adjust bwa single-end mapping for perfect matched alignment, i.e., ignore writing supplementary gapped or mismatched alignment to SAM. Do you have any directions on how to adjust relevant parameters? -B INT penalty for a mismatch [4] -O INT[,INT] gap open penalties for deletions and insertions [6,6] -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1] -h INT[,INT] if there are <INT hits with score >80% of the max score, output all in XA [5,200]

Do you think the above flags are something worth trying? thanks much, Zhenzhen