Unless you have updated your analysis settings, your sample will not show “PASS” in the QC section. The minimum number of unique reads is set to ensure there are no false negatives. Any fusions detected with a failed QC call may be real if they are classified as strong fusions; but fusion negative samples with a failed QC call may be too degraded or have too few reads to detect the fusion. Each lab can determine experimentally during validation whether or not this threshold needs to be adjusted.
This has proven to be a reasonable criterion for the success of the assay. However, users are encouraged to evaluate the results themselves and set their own cutoff.
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