How could I pass a specific argument to run pbrun germline pipeline or standalone process apply bqsr The arg is not currently listed in the option, but one of the parameters of gatk ApplyBQSR
This way I could also keep the original base quality score in the final out-put bam file. Basically to allow custom argument which available in the native (gatk) tool parameters, which will not affect/conflict to the gpu settings.
Possibility of tweaking specific python scripts in pbrun would do?
Thanks in advance.