Does BWA (BWA-MEM) care about the identity and coverage of the mapped reads?

Question

[culiu]

Hi All,

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???

Answer 1

[shaun]

You can tweak these features with the -B (mismatch penalty) -O and -E (gap penalties). You can see the coverage and mismatches in the resulting bam file and post-process it if you think the results are unsatisfying using samtools for instance.

[culiu]

Thanks for the reply, EvoBI!!

Yea. I also thought of this idea. But I still cannot go back to the exact settings (e.g., mapping identity = 90%, read coverage = 90%), right?

[DVA]

I wondered about that before as well, but ended up with the method @EvoBl mentioned. The accurate coverage won't be unveiled till after alignment anyway.