I am planning to jump from one old alignment method to BWA-MEM to analyse my 300 bp PE Illumina reads.
The old alignment method can filter the alignment result by identity and coverage of the mapped/aligned reads.
But in BWA-MEM, neither seems to have been mentioned.
Is it reasonable that the BWA-MEM can do split alignment and reduce the reference bias so it does not care about the relationships between the reads and the reference???