[troubleshooting] somatic pipeline

Hi there,

I followed the instruction from the doc somatic pipeline and got the following error.

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Error]: With --knownSites option, recalibration file will be generated. Please specify output
recalibration file.
[Parabricks Options Error]: Run with -h to see help

Could not run fq2bam as part of normal sample processing for somatic pipeline
Exiting pbrun ...

The command you provided seems to be missing the parameter --out-normal-recal-file for the normal sample.

Can you clarify?

After I fixed the error by adding the parameter --out-normal-recal-file, now I can run the somatic pipeline normally and get a vcf file.

Before vs After:

Best regards,
TJ Tsai