GC Bias Correction
GC Biases measure the relationship between GC content and read coverage across a genome. Biases can occur in library prep, capture kits, sequencing system differences, and mapping. Biases can result in difficulties calling CNV events. The DRAGEN GC bias correction module attempts to correct these biases.
The GC bias correction module immediately follows the target counts stage and operates on the *.target.counts.gz file. GC bias correction generates a GC bias corrected version of the file, which has a *.target.counts.gc-corrected.gz extension in the file name. The GC bias corrected versions are recommended for any downstream processing when working with WGS data. For WES, if there are enough target regions, then the GC bias corrected counts can also be used.
Typical capture kits have over 200,000 targets spanning the regions of interest. If your BED file has fewer than 200,000 targets, or if the target regions are localized to a specific region in the genome (such that GC bias statistics might be skewed), then GC bias correction should be disabled.
The following options control the GC bias correction module.
|
Option |
Description |
|---|---|
|
--cnv-enable-gcbias-correction |
Enable or disable GC bias correction when generating target counts. The default is true. |
|
--cnv-enable-gcbias-smoothing |
Enable or disable smoothing the GC bias correction across adjacent GC bins with an exponential kernel. The default is true. |
|
--cnv-num-gc-bins |
Specifies the number of bins for GC bias correction. Each bin represents the GC content percentage. Allowed values are 10, 20, 25, 50, or 100. The default is 25. |
