This could be tricky question. If my only goal is to call SNP, so when running BWA, any possibility I could only generate a small bam file where all alignments contain at least one potential variants? ie. The majority of alignments which perfectly match reference will be abandoned.
Or generally my question is, how can be bypass the "useless" perfect-matching alignments, so that only useful and small not-perfect-matching alignments are used? In this way we could optimize the whole pipeline.
Does BWA provide such related function? thx