The "Identify Variants" tool takes sequencing reads as input and returns identified variants in a Genome Browser View.
The tool runs an internal workflow that first maps the sequencing reads to the human reference sequence. Next, it runs a local realignment that is used to improve the variant detection that comes after the local realignment. Two different variant callers are used; the "Low Frequency Variant Detection" caller that is used to call small insertions, deletions, SNVs, MNV, and replacements, and the "InDel and Structural Variants" caller that calls larger insertions, deletions, translocations, and replacements. By the end of the variant detection, variants that have been detected by the "Low Frequency Variant Detection" caller with an average base quality smaller than 20 are filtered away.
A detailed mapping report is created to inspect the overall coverage and mapping specificity in the targeted regions.