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High-level schematic of the CGES pipeline running from top to bottom. Each of the four branches applies a separate caller to the same input alignment (BAM) files. The basic filter consists of a BED target file defined by the capture, and a minimum QUAL of 10. Variant normalization entails standardizing the representation of more complex alleles such as indels. The final product is a multi-sample variant call format (VCF) file and associated quality metrics
