Sequence variant baselines
The filters that are used in Ion Reporter™ Software remove most sequencing errors. While variant calling filters in the software suppress sequencing errors, it is possible that some errors can pass through the filters and be reported as false positives. However, in somatic panels, sequencing errors that survive filtering are reported as false positives that require investigation.
To reduce the number of potential false positives, you can create a sequence variant baseline for panels that detect somatic variants.
A sequence variant baseline is BED file that contains a list of alleles that are known sequencing errors. The baseline file records detailed properties for each sequencing error. The errors and properties are based on known germline normal samples. When added to a workflow, the baseline detects and filters out the errors in sequencing that could lead to false positive variant calls.