6-column target regions BED file format

The 6-column target regions 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 track line includes these tab-separated fields:

Field

Type

Description

name

(Optional)

String

A unique design identifier.

description

(Optional)

String

A description of the design.

type

(Required)

String

Must be bedDetail (without quotes).

ionVersion

String

Introduced in the Torrent Suite™ Software 4.0 release.

The following is an example track line: 


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

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)

The name of the chromosome. This name must be an exact match with a chromosome in the reference.

chromStart

Unsigned int64

The starting position of the feature (zero-based).

chromEnd

Unsigned int64

The 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

A customer-specified ID. If missing, set to '.'. This field is not used.

GeneSymbol

String

The 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
Related Topics
Parent topic: Target regions BED file formats