Scaled reads for a Structural Variation event
If false positives are a concern for the data that is being analyzed, then you can scale the Linked Reads, which applies a normalization factor to set a scaled threshold for filtering the report. Two thresholds—the number of Total Aligned Reads and the number of Scaled Linked Reads—must be met for a Structural Variation event to be initially included in the report. The default value for Total Aligned Reads is 2,000,000.
• If Total Aligned Reads >= <y>, then the Scaled Linked Reads threshold = <x> / Total Aligned Reads x 1,000,000 (normalization factor) and then use the scaled threshold to filter the report.
• 400 “unscaled” Linked Reads / 2,000,000 Total Aligned Reads x 1,000,000 = 200 Scaled Linked Reads. Include reads in the report.
• 200 “unscaled” Linked Reads / 2,000,000 Total Aligned Reads x 1,000,000 = 100 Scaled Linked Reads. Filter reads from the report.
• If Total Aligned Reads <= <y>, then do not scale the threshold and use <x> to filter the report on the Linked Reads directly.
• 20 unscaled Linked Reads / 100,000 Total Aligned reads x 1,000,000 results in the display of 200 Scaled Linked Reads, but because the Total Aligned Reads threshold fails, use original 20 unscaled Linked Reads. Filter reads from report.