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Fusions CSV
File name: {Sample_ID}_Fusions.csv
Contains all candidate fusions identified by the RNA analysis pipeline. Two key output columns, Filter and KeepFusion, are described below.
The following table describes the output found in the Filter columns. The output is either a confidence filter or information only as indicated.
If none of the filters described below are triggered, the filter column will display PASS.
|
Filter |
Description |
|
Imprecise |
A low-resolution candidate, not an assembled fusion call. (Confidence filter) |
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RepeatOverlap |
The fusion is tagged as overlapping with a repeat region. Only used as a confidence filter for non-uniquely mapping fusion candidates, otherwise information only. (Confidence filter) |
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WeakBreakend |
The read/alignment evidence on one side of the fusion is weak. Usually this filter indicates that the reads only overlap the fusion by a few base pairs. Alternatively, it can indicate too much homology (no unique sequence). (Confidence filter) |
|
Homology |
The fusion contig is a substring of another fusion contig. (Confidence filter) |
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DuplicateContig |
The 2 contigs of the fusion are the same contig. (Confidence filter) |
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ContigIntragenic |
The realignment of half-contigs produces alignments that map to the same gene on both sides (or within 1kb if unannotated). (Confidence filter) |
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LowQ |
Fusion supporting reads (unique) < 5 (+ 1 for every 10 million reads over 16 million reads). (Confidence filter) |
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LowDupeReads |
Fusion supporting reads (duplicate) < 5.(Confidence filter) |
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NonExonic |
Fusion breakpoint does not fall within an exon. (Information only) |
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LocalContigAlign |
Contig realignment found a nonfusion alignment for this contig. (Information only) |
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LowFusionRatio |
Few strong evidence reads compared to wild-type reads. (Information only) |
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NoReferenceReads |
No reads on either side of the presumed breakpoint are marked as reference (structurally normal) reads. (Information only) |
The KeepFusion column of the output has a value of True when the RNAFusionFilter score is ≥ to 0.45 and none of the confidence filters are triggered.
Candidate fusions from the splice variant caller are listed in this output with relevant supporting information but are not considered high confidence.
See the headers in the output for more information about each column.
NOTE
When using Microsoft Excel to view this report, genes with dates in the mm-dd format (MARCH1) are converted to dd-mm (1-Mar).
For Research Use Only. Not for use in diagnostic procedures.