Hotspots file

A hotspots file contains a list of positions on the genome and when configured in a workflow affects the analysis results. For each position during variant calling:

Evidence for a variant is examined at that position (without regard to the hotspots positions) and a call is made.
Then the hotspots positions are examined. At each position listed in the file, if a variant is not already called, then one of the following variant calls is added:
- REF Homozygous reference
- NOCALL A variant is not called at this position (for instance, because of lack of coverage)
The filtering metrics for each position are reported in the output VCF file, including for NOCALL.

By default the variantCaller plugin calls variant candidates at hotspot positions with more sensitivity than candidates at other positions. You can customize certain variantCaller parameters separately for hotspot candidates.