I was wondering if anyone has experience running Pisces and/or Octopus on whole-exome sequencing samples (100-200x) for somatic variant calling.
Eventually, I would like to compare the variants from Pisces/Octopus with those from Mutect2 (potentially a consensus approach involving all 3?).
Any insight/advices/warnings would be helpful. Thank you!
- From my initial runs with samples (tumor-only calling), Pisces seems to be generating many more variants compared to octopus, but majority of variants (80-90%) from Octopus are subsets of those called by Pisces (To my knowledge, raw Pisces VCFs requires filtering).