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 the software runs through major analysis phases:
The following table describes how Torrent Suite™ Software output files are used in Ion Reporter™ Software analyses.
|
BAM file |
TS analysis pipeline |
Any except annotation-only |
|
VCF file |
TS Variant Caller (variantCaller) plugin |
Annotation-only |
The IonReporterUploader plugin by default uploads both the BAM file and the VCF file from the Ion 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 analysis workflow runs this phase by itself. (All other analysis workflows include the annotation phase as their last analysis phase.) The annotation-only analysis workflow requires as input a VCF file, which can be generated from either an Ion Reporter™ Software analysis, a variantCaller plugin analysis, or a different source.