HotSpots File Format

The track line is required in a HotSpots BED file. The following is an example track line:

The track line includes these tab-separated fields:

Field	Type	Description
Name	string	A unique design identifier. Optional.
Description	string	Description of the design. Optional.
Type	string	Must be "bedDetail" (without quotes). Required.
db	string	The UCSC Assembly ID. Optional.
reference	string	The Torrent Server reference ID. Optional for hg19. Required for GRCh38.

The following is an example track line:

track name="ASD270245" description="HotSpots locations for AmpliSeq ASD270245" type=bedDetail db=hg38 reference=GRCh38.p2

In HotSpots BED files, the coordinates lines require the following tab-separated fields:

Field	Type	Description
chrom	string (chars >= 0x20, other than \tab)	Name of the chromosome. This name must be an exact match with a chromosome in the reference.
chromStart	unsigned int64	Starting position of the feature (zero-based).
chromEnd	unsigned int64	Ending position of the feature (not inclusive). Must be greater than chromStart.
HotSpotName	string	This ID is either the COSMIC ID, dbSNP ID, or user-defined. If missing, the following string is used "chrom" + ":" + "chromStart" + "-" + "chromEnd"
HotSpotAlleles	string	This field describes the variant, using this format (see examples below): `REF=` reference_allele ; `OBS=` observed_allele ; `ANCHOR=` base_before_allele
AmpliconID	string	Amplicon ID. If missing, the following string is used "chrom" + ":" + "chromStart" + "-" + "chromEnd"