Copy Number Variant Calling
The CRAFT copy number variant caller performs amplification, reference, and deletion calling for target amplification genes within the assay. This calling is based on the calculated fold change value. Fold change is defined as the median normalized bin count value for a target gene over the median bin count value of the entire panel. The inputs are in BAM format and the outputs are VCF files. Deletion is marked with the LowValidation filter in the VCF file because they have only been tested with in silico data sets.