Torrent Suite™ Software output and Ion Reporter™ Software analysis phases

Typically the BAM file output of your Torrent Suite™ Software analysis is uploaded to Ion Reporter™ Software and then Ion Reporter™ Software runs through its major analysis phases as follows:

Mapping
Variant calling
Annotation

This table shows how Torrent Suite™ Software output files are used in Ion Reporter™ Software analyses:

Torrent Suite™ Software output file	Output from this Torrent Suite™ Software analysis phase	Input to this Ion Reporter™ Software workflow
BAM file	TS analysis pipeline	Any except annotation-only
VCF file	TS Variant Caller (variantCaller) plugin	Annotation-only

The Ion Reporter™ Uploader plugin by default uploads both the BAM file and the VCF file from your Torrent Server to Torrent Suite™ Software.

The following table describes the input and output file types for the analysis phases:

Analysis phase	Input file type	Output file type
Mapping	BAM file (mapped or unmapped)	Mapped BAM file
Variant calling	Mapped BAM file	VCF file
Annotation	VCF file (with or without annotations)	Annotated VCF file

Each output file type is required as input to the next analysis phase. In almost all cases, the Ion Reporter™ Software analysis phases are performed in order.

The exception is the annotation phase. The annotation-only workflow runs this phase by itself. (All other workflows include the annotation phase as their last analysis phase.) The annotation-only workflow requires as input a VCF file, which can be generated from either a Ion Reporter™ Software analysis, a Ion Reporter™ Software analysis variantCaller plugin analysis, or a different source.