6-column Target Regions BED File Format

The 6-column BED file format is used when some or all of the gene names are known. BED files that are generated by AmpliSeq.com use this 6-column format.

The track line is required in a 6-column target regions BED file. The following is an example track line:


track name="ASD270245" description="AmpliSeq Pool ASD270245" ? type=bedDetail

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.
ionVersion	string	Introduced in the Torrent Suite™ Software 4.0 release.

In a 6-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"
ID	string	Customer-specified ID. If missing, set to '.'. This field is not used currently.
GeneSymbol	string	Gene name. If missing, set to '.'.

Partial example of a 6-column target regions BED file:


? track name="ASD270249_v1" description="AmpliSeq Pool ASD270249" type=bedDetail chr9 133738312 133738379 AM73150 NM_005157 ABL1 chr9 133747484 133747542 AM73075 NM_005157 ABL1 chr9 133748242 133748296 AM73104 NM_005157 ABL1 chr9 133748388 133748452 AM491413 NM_005157 ABL1 chr9 133750331 133750405 74743 NM_005157 ABL1 chr9 133738312 133738379 73150 NM_007313 ABL1 chr9 133747484 133747542 73075 NM_007313 ABL1 chr9 133748242 133748296 73104 NM_007313 ABL1 chr9 133748388 133748452 491413 NM_007313 ABL1 chr9 133750331 133750405 74743 NM_007313 ABL1 chr14 105246407 105246502 329410 NM_001014431 AKT1 chr14 105246407 105246502 329410 NM_001014432 AKT1 chr14 105246407 105246502 329410 NM_005163 AKT1 chr2 29432658 29432711 34014 NM_004304 ALK