How to pass argument not listed in the option to run pbrun germline pipeline or standalone process apply BQSR

Hi All,

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 --emit-original-quals.

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.

Best
Justin

Hi Justin,

We do not support all the GATK options right now but the popular options and any feedback we get about the option from the community is greatly appreciated.
Its not possible to tweak the python scripts to achieve this. We will try our best to include –emit-original-quals in the future release.

Thanks,
Ashish