Track line

The track line is required in the Target Regions BED file. The following is an example track line: 


track name="Fusions 2.6" description="AmpliSeq RNA" type=bedDetail ionversion="4.0"

The track line includes these tab-separated fields:

Table 1.

Field

Type

Description

name

(Optional)

String

A unique design identifier.

description

(Optional)

String

The description of the design.

type

(Required)

String

Must be "bedDetail" (without quotes).

ionversion

String

Introduced in the Torrent Suite™ Software 4.0 (Ion AmpliSeq™ Designer 3.0 and higher fixed panels).

When set to "4.0", indicates that the BED file supports the Extended BED Detail format..

Optional. This field relates to only the BED file format version, not the version of panel designs.

Columns

This format includes eight required columns that are separated by a tab (\t) character.

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 (Insert Start not the Amplicon Start). Must be zero-based.

chromEnd

Unsigned int64

The ending position of the feature (not inclusive) (Insert End not the Amplicon End). Must be greater than chromStart.

AmpliconID

String

The Amplicon ID. If missing, the following string is used "chrom" + ":" + "chromStart" + "-" + "chromEnd"

Score

Unsigned int64

Score. If missing, set to '.'. This field is not used.

Strand

String (+ or -)

Strand. If unknown, set to '+'.

ID

String

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

Key-value pairs

String

Multiple attributes specified as semicolon separated key-value pairs. See below for specific key-value pairs. All of these KVPs are required for fusions designs files, but most of these are optional for other White Glove designs.

The genomic (hg19) coordinates provided in the key-value pairs must represent the entire amplicon sequence. If you want to generate the fusions mapping reference FASTA file from the BED file, all the information that is needed should be available in the BED file.

The following key-value pairs are supported.

Key

Value

Example

TYPE

The type of the event. Allowed values:

  • Fusion

  • CONTROL or ExpressionControl

  • Driver_Gene or 5p3pAssay

  • GeneExpression

  • RNA_Hotspot

TYPE=Fusion

FP_TRANSCRIPT_ID

The transcript ID for the 5′ gene partner.

This key value pair is only for fusion type targets.

FP_TRANSCRIPT_ID=ENSG00000156735

TP_TRANSCRIPT_ID

The transcript ID for the 3′ gene partner. This field is absent for CONTROL type amplicons.

This key value pair is only for fusion type targets.

TP_TRANSCRIPT_ID=ENSG00000077782

BREAKPOINT

The position in the sequence for the breakpoint. Applicable to only fusion type amplicons. This position is number of bases from the Insert start, not the Amplicon Start.

BREAKPOINT=56

FP_GENE_ID

The name of the 5′ gene partner in the fusion.

This key value pair is only for fusion type targets.

FP_GENE_ID=BAG4

FP_GENE_STRAND

The strand for the 5′ gene partner. Allowed values are '+' and '-'.

This key value pair is only for fusion type targets.

FP_GENE_STRAND=+

FP_EXON_NUMBER

The exon number in the 5′ gene. Use comma-separated values if the amplicon spans multiple exons.

This key value pair is only for fusion type targets.

FP_EXON_NUMBER=2

TP_GENE_ID

The name of the 3′ gene partner in the fusion. This field is absent for CONTROL type amplicons.

This key value pair is only for fusion type targets.

TP_GENE_ID=FGFR1

TP_GENE_STRAND

The strand for the 3′ gene partner. Allowed values are '+' and '-'. This field is absent for CONTROL type amplicons.

This key value pair is only for fusion type targets.

TP_GENE_STRAND=-

TP_EXON_NUMBER

The Exon number in the 3′ gene. Use comma-separated values if the amplicon spans multiple exons.

This key value pair is only for fusion type targets.

TP_EXON_NUMBER=6

FP_CHROM

The chromosome of the 5′ gene.

This key value pair is only for fusion type targets.

FP_CHROM=chr8

FP_START

The start position for the 5′ segments. Use comma-separated values if there are multiple segment Starts.

This key value pair is only for fusion type targets.

FP_START=38050257

FP_END

The end position for the 5′ segments. Use comma-separated values if there are multiple segment Ends.

This key value pair is only for fusion type targets.

FP_END=38050313

TP_CHROM

The chromosome of the 3′ gene. This field is absent for CONTROL type amplicons.

This key value pair is only for fusion type targets.

TP_CHROM=chr8

TP_START

The start position for the 3′ segments. Use comma-separated values if there are multiple segment Starts.

This key value pair is only for fusion type targets.

TP_START=38283673

TP_END

The end position for the 3′ segments. Use comma-separated values if there are multiple segment Ends.

jTP_END=38283763

HOTSPOT_POSITION

The genomic coordinate of the hotspot snp covered by the amplicon. Use comma-separated values if multiple hotspots are covered by the amplicon.

HOTSPOT_POSITION=38283769

CHROM

The chromosome name of the target region. This key is for all non-fusion type targets. For fusion targets, we have FP_CHROM and TP_CHROM.

CHROM=chr8

GENE_ID

The name of the gene for nonfusion type targets. For fusion targets, we have FP_GENE_ID and TP_GENE_ID.

GENE_ID=LMNA

TRANSCRIPT_ID

The transcript Id for nonfusion type targets. For fusion targets, we have FP_TRANSCRIPT_ID and TP_TRANSCRIPT_ID.

TRANSCRIPT_ID=ENST00000389048

GENE_STRAND

The strand of the gene. This key is for all nonfusion type targets. For fusion targets, we have FP_GENE_STRAND and TP_GENE_STRAND.

GENE_STRAND=+

EXON_NUM

The exon number(s) in the gene. Use comma-separated values if the amplicon spans multiple exons. For fusion targets, we have FP_EXON_NUM and TP_EXON_NUM.

EXON_NUM=3,4

START

The start position of the target segment. Use comma-separated values if there are multiple segment starts in genomic space. This key is for all nonfusion type targets. For fusion targets, we have FP_START and TP_START.

START=53586113,53585786

END

The end position of the target segment. Use comma-separated values if there are multiple segments in genomic space. This key is for all nonfusion type targets. For fusion targets, we have FP_END and TP_END.

END=53586228,53585803

MIN_READ_COUNT

The minimum number of reads needed to call the particular target as present/absent. This value is optional and if present, overrides the universal minimum read count threshold (for example, 20).

Example usage—For EGFR deletion assay, we would use a higher read count threshold (greater than 20).

MIN_READ_COUNT=100

Related Topics
Parent topic: RNA fusions BED file formats and examples