All sequencing libraries from multiple GCCs for each donor are provided as high-depth input to each caller. PacBio data is also provided for long-read calling when available.
TNHaplotyper2 is run in tumor-only mode with default parameters.
Strelka2 is the only caller run in a paired mode. Because SMaHT investigates normal tissues rather than tumor-normal pairs, Strelka2 uses a fixed benchmarking tissue (ST002-1D, ~220×) as a pseudo-normal comparator for all production tissues.
RUFUS is run in single-sample mode and uses a panel of normals approach to filter false positives.
Though longcallD supports both PacBio and ONT run modes, SNV calling uses only the PacBio mode. Higher false-positive rates were observed in ONT-based SNV calls, so ONT longcallD output is excluded from the candidate set.