Reg: Usage of somatic pipeline

Hi team,

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…

Hello poornachandraroyal33,

For the whole pipeline command, can you let me know in what way it is not working? Which command are you running and how is it failing?

For CNVkit, the error message is correct, the current release is not supporting CNVkit. Can you point me to where in the documentation CNVkit is referred to? I will get this corrected.

Many thanks,
Mike

Hi Mevella,

Thanks for the reply.

For the point 1:
We are using following command for running the whole somatic pipeline:

pbrun somatic --ref genome.fa --in-tumor-fq sample.fastq1.gz sample.fastq2.gz --out-tumor-bam sample_output_somatic.bam --knownSites Homo_sapiens_assembly38.known_indels.vcf.gz --num-cpu-threads 16 --tmp-dir --num-gpus 1 --out-vcf sample_output_somatic.vcf

The pipeline is working perfectly fine without failing. However, we would like to know ‘is there is any specific way to restrict the variant calling process using the interval file similar to GATK-mutect2’ ?
Also, this filtering option is available with the ‘pbrun mutectcaller’ command as shown below (-intervel-file):

pbrun mutectcaller --ref genome.fa --in-tumor-bam sample_output_recal.bam --out-vcf sample_output.vcf --tmp-dir temp –interval-file AgilentV7.bed --tumor-name sample

For the point2:
CNVkit is available for the v3.0.0 as mentioned below:


However same is not present with v2.5.0, which is provided for free trail.

Hi poornachandraroyal33,

For the point 1:
Right now --interval-file is only available for mutectcaller.

For the point 2:
CNVkit is not available for Free for Covid-19 version, we will update the documentation

Thanks
Myrieme