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.
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_IDs.
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.
