Only header but no mutations were present in varscan vcf output.

[EvaPang2022]

Hi,

I have matched tumour-normal samples, and I am currently calling somatic variants using strelka2, mutect2 and varscan through the next-gen bcbio pipeline. I did not meet any error message during the process.

But in the varscan vcf file, only header but no any mutations (reject/pass) were present, while mutect2 and strelka2 did report a lot of somatic mutations.

May I know what are the possible reasons here?

version: bcbio-nextgen,1.2.9

Thanks & Regards!