There can be multiple reasons for the variants that were called in v1 to be not called in v2. The reason for why a variant was dropped is available in the candidate variants table in the QC tab. Each reason is in turn defined on the Definitions tab, except for the one below:
- Dropped by SPARC - This would be the main reason for a variant to be dropped by CIS pipeline. The SPARC phylogeny tool drops a variant when due to its missing data, mutated cells from another variant are entirely dropped.