Extended BED Detail format

Ion AmpliSeq™ Designer 3.0 and later uses Extended BED Detail format for the following fixed panels:

CCP
CFTR
CHP v2
Ion AmpliSeq™ Exome

New fixed panels that are introduced for Ion AmpliSeq™ Designer 3.0 and later also follow this format. Other panels, and all panels from previous releases, do not use this format.

The Extended BED Detail format contains two additional fields (at the end of each line).

Name	Values	Description
`Id`	Any string supplied by the user or '.'	A user-supplied name or identification for the region.
`Description`	The key-value pairs separated by semicolon, or '.' if empty	Contains a '.' or one or more of the following: `GENE_ID=` `Pool=` `SUBMITTED_REGION=` These key-value pairs are described in the next table.

Name

Values

Description

Id

Any string supplied by the user or '.'

A user-supplied name or identification for the region.

Description

The key-value pairs separated by semicolon, or '.' if empty

Contains a '.' or one or more of the following:

GENE_ID=
Pool=
SUBMITTED_REGION=

These key-value pairs are described in the next table.

The following table lists the keys and describes the key-value pairs that are supported.

Key	Description
`GENE_ID`	A gene symbol or comma-separated list of gene symbols. If no gene symbol is available, this key is absent. Example: `GENE_ID=brca1` Example: `GENE_ID=brca1, ret`
`Pool`	The Ion AmpliSeq™ Designer pool or pools containing this amplicon. Example: `Pool=2` If an amplicon is present in multiple pools, the pools are delimited with "," (comma), with the primary pool listed first. For example, if an amplicon is present in pools 1 and 3, and 1 is the primary pool, the entry is `Pool=1,3`. Single-pool designs do not include the `Pool=` key-value pair.
`SUBMITTED_REGION`	The region name provided during the Ion AmpliSeq™ Designer design process. If a region name is not provided, this key is absent. Example: `SUBMITTED_REGION=Q1`
`CNV_ID`	A gene symbol used to specify a copy number region for the cnv pca algorithm. This takes precedence over the `GENE_ID` and once CNV_ID can span multiple `GENE_ID`s.
`CNV_HS`	A CNV region hotspot. This can be a value of either 0 or 1. 1 reports as a hotspot (HS) in the output VCF file from the CNV PCA algorithm. 0 is not reported as HS.

The Extended BED Detail format requires a track line with both type=bedDetail and ionVersion=4.0. The Torrent Suite™ Software BED validator treats the Id and Descriptor fields as optional.

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Extended BED Detail format