increase BWA sensitivity

Question

[sacha]

Hi,

I would like to remove human reads from a metagenomics NGS dataset ( fastq ). Which parameter from bwa mem can I change to increase the sensibility ? ( I would like to align more reads )
Penality score ? Gap open ? Clipping penality ?

[WouterDeCoster]

You mean sensitivity, probably?

[GenoMax]

I would like to align more reads

Will that need a decrease in sensitivity (and specificity?).

[WouterDeCoster]

@sacha Don't think there is a reason to delete this thread...?

Answer 1

[h.mon]

Personally, I would use the RemoveHuman approach from BBMap.

Are you trying to clean Illumina reads? BWA is already pretty sensitive, you will probably increase false positives if you tweak the parameters. If you want increased sensitivity, with (I believe) the same precision, you can try vg: