Description
CNV detection is a first step towards full Structural Variant detection. 42Genetics CNV uses the coverage of two samples, or a sample and a group of samples compiled into a GCO (42Genetics Coverage) file. It computes a normalized differential between the two inputs. The sample input is obtained from the GAR file. The GAR file has a separate section, which holds coverage data that is collected during read alignment. This method allows CNV to be completed in seconds instead of hours or days with other tools. The group coverage can be compiled from a set of GAR files. The average and standard deviation of the group can be used to make a statistical call for GAIN, LOSS or NORMAL for a segment of the genome. Segments can be as small as 100 bases.
