I have matched samples from three tissues of an individual and I am trying to prioritize the pathogenic variants depending upon phenotype terms encoded by HPO. For my variant calling I have used Mutect2, and Varscan v2.3.9. but none of the called somatic variants from both the tools are common, and the vcf generated from varscan classifies 3000 variants as somatic while I get only 31 variantions that have passed the filters of mutect and called as somatic variants. both the tools were run in the default settings provided by the manufacturer. it will be really helpful if you can suggest me any tools which will be good to use with MuTect2, and methods to filter out the variants generated to reduce the no of false positive results. Thanks in advance.
the number of variants in the varscan output is my real cause of worry.
From the author of varscan, you should filter the results:
Because these are usually rare events, their call sets are often enriched for false positives.
The bam-readcount utility (https://github.com/genome/bam-readcount)
The fpfilter.pl accessory script (https://sourceforge.net/projects/varscan/files/scripts/)