wdl bwa parameters

[mcgml]

Hi

Thanks for releasing this WDL script. I noticed the bwa parameters are: bwa_commandline="bwa mem -K 100000000 -p -v 3 -t 16 $bash_ref_fasta"

What is the -K flag for? it is not defined in the bwa manual. Also is -M missing?

Thanks
Matt

[vdauwera]

Hi @mcgml, apologies for the late reply. I don't know the answer to this but will consult the team.

@sooheelee, do you happen to know about this -K parameter? I'm not finding any reference to it anywhere either. If you don't, can you please ask Heng at office hours tomorrow?