Does BWA (BWA-MEM) care about the identity and coverage of the mapped reads?
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6.0 years ago
culiu ▴ 20

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???

bwa bwa-mem alignment mapping reference • 2.9k views
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6.0 years ago
shaun ▴ 80

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.

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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?

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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.

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