Extended BED Detail format

Beginning with the 3.0 release, AmpliSeq.com uses this format for the following fixed panels:

CCP
CFTR
CHP v2
Ion AmpliSeq™ Exome

New fixed panels introduced after the AmpliSeq.com 3.0 release 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, if supplied by the user, or '.'	User-supplied name or id for the region.
Description	key-value pairs separated by semicolon, or '.' if empty	Contains a '.' or one or more of the following: GENE_ID= SUBMITTED_REGION= Pool= These key-value pairs are described in the next table.

Name

Values

Description

Any string, if supplied by the user, or '.'

User-supplied name or id for the region.

Description

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

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

GENE_ID=
SUBMITTED_REGION=
Pool=

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

This table describes the key-value pairs that are supported in the Description column:

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 Ampliseq.com pool or pools containing this amplicon. Example: Pool=2 If an amplicon is present in multiple pools, the pools are delimited with "," a 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 by the user during theAmpliSeq.com 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 will take precedence over the GENE_ID and once CNV_ID can span multiple GENE_IDs.
CNV_HS	A CNV region hotspot. This can be a value of either 0 or 1. A 1 will report as a hotspot (HS) in the output VCF file from the CNV PCA algorithm. A 0 will not be 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 these fields (Id and Descriptor) as optional.