Our organization recently acquired the free license for Parabricks to test the performance.
While running the somatic pipeline provided, I realized that interval file (bed file) option is not available for the somatic pipeline to restrict the variant calling processes only to the specified regions. whereas this interval file option is available for mutectcaller (which is a part of somatic pipeline) .
Also, in the the documentation CNVkit is available in the Parabricks suite, however , when I am trying to run the CNVkit, it throws an error saying CNVkit is ‘not supported in this release. Exiting’
Kindly let us know how to use the bed file for variant calling in the somatic pipeline and run the CNVkit…
pbrun version: v2.5.0
Thanks in advance…