fusions.csv

The fusions.csv file is generated from fusion calls based on the Fusion target type. The file contains the columns listed below. The rows are sorted by score in descending order. Entries with scores below 2 are not included.

Column

Description

Target ID

The unique identifier for the fusion target.

Target Number

Target number from the manifest. Negative numbers indicate off-targets while positive numbers indicate on-targets.

Gene A

Gene symbol of fusion partner A.

Gene B

Gene symbol of fusion partner B.

Transcript ID A

Transcript ID of fusion partner A.

Transcript ID B

Transcript ID of fusion partner B.

Exon A

Exon(s) of fusion partner A.

Exon B

Exon(s) of fusion partner B.

Breakpoint A

The breakpoint of fusion on gene A with genomic coordinates <chrom>:<position>.

Breakpoint B

The breakpoint of fusion on gene B with genomic coordinates <chrom>:<position>.

Supporting Reads

The target read count.

Score

The score is calculated using the read count of the target and the total read count of the sample:

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Where totalreadcount is the number of reads mapped to all the targets in the manifest. The normalized read count is centered by 32.74276 and scaled by 254.8784 to produce a z-score-like score, where the two constants were learned from control samples without known fusions.

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The higher the score, the stronger the evidence of a fusion being present in the sample in question. Potential fusions with scores below 1 are not included in the fusions.csv file and potential fusions with scores lower than the 4 are filtered as LowScore.

Filter

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OffTarget—The target is an off-target.

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LowScore—The score is less than the FusionScoreCutoff setting.

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PASS—The target is an on-target and the sore is at least the FusionScoreCutoff setting.

Fusion Call

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NoCall—The score is less than the FusionScoreCutoff setting.

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Present—The target read count is greater than 0 and the score is at least the Fusion ScoreCutoff setting.

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fusions.csv