track name=

"Fusions 2.6"

description=

"AmpliSeq RNA"

 type=bedDetail ionversion="4.0"

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 (AmpliSeq.com 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 BED File format version only, not the version of panel designs.

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

chromEnd

unsigned int64

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

AmpliconID

string

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 currently.

Strand

string (+ or -)

Strand. If unknown, set to '+'.

ID

string

Customer-specified ID. If missing, set to '.'. This field is not used currently.

Key-value pairs

string

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

TYPE

Type of the event. Allowed values:

• Fusion

• CONTROL or ExpressionControl

• Driver_Gene or 5p3pAssay

• GeneExpression

• RNA_Hotspot

TYPE=Fusion

FP_TRANSCRIPT_ID

Transcript ID for the Five Prime Gene partner. This key value pair is only for Fusion type Targets.

FP_TRANSCRIPT_ID=ENSG00000156735

TP_TRANSCRIPT_ID

Transcript ID for the Three Prime 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

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

Name of the Five Prime Gene partner in the Fusion.This key value pair is only for Fusion type Targets.

FP_GENE_ID=BAG4

FP_GENE_STRAND

Strand for the Five Prime Gene partner. Allowed values are '+' and '-'.This key value pair is only for Fusion type Targets.

FP_GENE_STRAND=+

FP_EXON_NUMBER

Exon number in the Five Prime Gene. Use comma separated values if there the Amplicon spans multiple Exons.This key value pair is only for Fusion type Targets.

FP_EXON_NUMBER=2

TP_GENE_ID

Name of the Three Prime 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

Strand for the Three Prime 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

Exon number in the Three Prime Gene.Use comma separated values if there the Amplicon spans multiple Exons. This key value pair is only for Fusion type Targets.

TP_EXON_NUMBER=6

FP_CHROM

Chromosome of the Five Prime Gene.This key value pair is only for Fusion type Targets.

FP_CHROM=chr8

FP_START

Start position for the Five Prime 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

End position for the Five Prime 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

Chromosome of the Three Prime Gene. (This field is absent for CONTROL type amplicons.).This key value pair is only for Fusion type Targets.

TP_CHROM=chr8

TP_START

Start position for the Three Prime 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

End position for the Three Prime Segments. Use comma-separated values if there are multiple segment Ends.

TP_END=38283763

HOTSPOT_POSITION

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

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

Name of the Gene for non-fusion type targets. For Fusion targets, we have FP_GENE_ID and TP_GENE_ID.

GENE_ID=LMNA

TRANSCRIPT_ID

Transcript Id for non-fusion type targets. For fusion targets, we have FP_TRANSCRIPT_ID and TP_TRANSCRIPT_ID.

TRANSCRIPT_ID=ENST00000389048

GENE_STRAND

Strand of the Gene. This key is for all non-fusion type targets. For fusion targets, we have FP_GENE_STRAND and TP_GENE_STRAND.

GENE_STRAND=+

EXON_NUM

Exon number(s) in the Gene. For fusion targets, we have FP_EXON_NUM and TP_EXON_NUM.Use comma separated values if there the Amplicon spans multiple Exons.

EXON_NUM=3,4

START

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

START=53586113,53585786

END

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

END=53586228,53585803

MIN_READ_COUNT

Minimum number of reads needed to call the particular target as present/absent. This value is optional and if present, it will override the universal minimum read count threshold (eg: 20). Example Usage: For EGFR deletion assay, we would use a higher read count threshold (greater than 20).

MIN_READ_COUNT=100