adding passing options to bwa mem

brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

https://arxiv.org/abs/1401.1129

MIT License

139 stars 53 forks source link

adding passing options to bwa mem #20

Closed avilella closed 5 years ago

avilella commented 8 years ago

When I run bwa-meth, it calls bwa-mem with these parameter set:

bwa mem -T 40 -B 2 -L 10 -CM

Would it be possible to pass-through the -T/B/L options to the script to tune it to the desired options by the user?

brentp commented 8 years ago

Yeah, I should add this, but didn't want to replicate all of the options. For now, you can just edit bwa-meth.py directly. I found that changing those doesn't affect the results much, but I wanted to have higher penalties.

avinashs commented 5 years ago

Follow up question on this old issue.. but curious if you had a specific reasoning for fixing the default penalties that you did. Particularly, it seems like bwa-meth is highly incentivized to allow mis-matches in an alignment than resort to clipping. Is there something inherent about Bisulphite sequencing data that requires that clipping should be discouraged? Or was it just a heuristic? Thanks!

brentp commented 5 years ago

I can't remember why I did this, but it's possible to send your own arguments via the command line to override the defaults. The penalties I made up are not that different from bwa mem defaults so I doubt it matters much.