4-column Target Regions BED File Format

The 4-column BED file format is used when gene names are not known and some or all amplicon IDs are known.

The track line is optional. If present, it includes these tab-separated fields:

Field	Type	Description
Name	string	A unique design identifier. Optional.
Description	string	Description of the design. Optional.

The following is an example track line:

track name="ASD270245" description="AmpliSeq Pool ASD270245"

In a 4-column target regions BED file, 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.
AmpliconID	string	Amplicon ID. If missing, the following string is used "chrom" + ":" + "chromStart" + "-" + "chromEnd"

Partial example of a 4-column target regions BED file:

chr9 133738312 133738379 amplID73150 chr9 133747484 133747542 amplID73075 chr9 133748242 133748296 amplID73104 chr9 133748388 133748452 491413 chr9 133750331 133750405 74743 chr9 133738312 133738379 73150 chr9 133747484 133747542 73075 chr9 133748242 133748296 73104 chr9 133748388 133748452 491413 chr9 133750331 133750405 74743 chr14 105246407 105246502 329410 chr2 29432658 29432711 34014