The final confidence designations are either PASS or LowEvidence and are found in the FILTER field of the output VCF. An EvidenceScore integer INFO field records the number of Cross* flags present.
EvidenceScore = CrossTech + CrossCaller + CrossCore + CrossTissue
Each flag contributes 1 if present, 0 if absent, giving a score of 0–4. This field is preserved in the final VCF to allow downstream analyses to apply additional stratification — for example, requiring EvidenceScore ≥ 2 for the most stringent call sets, or requiring CrossTech specifically for long-read-confirmed calls.
Variants with EvidenceScore ≥ 1 receive a FILTER of PASS. These variants have been corroborated by at least one independent axis of evidence: a second sequencing technology, a second caller, a second core, or a second tissue. The specific combination of flags is retained in the INFO fields.
Variants with EvidenceScore = 0 receive a FILTER of LowEvidence. These variants cleared all hard filters (steps 1–8) and passed the statistical read-support and germline checks, but were observed in only a single technology, by a single caller, in a single core, and in a single tissue. They represent somatic candidates that cannot be distinguished from rare artifacts on the basis of corroboration alone. They are retained in the output for completeness but should be treated with caution, particularly in tissues without PacBio coverage where long-read corroboration is unavailable.