CNV analysis and Report page overview

This pipeline assess copy number variation throughout the genome using the BAM file(s) output by our Alignment/QC workflow, and provides an interactive visualization to browse potential CNVs.


-a chromosome-level browser for visualizing CNV calls

Output Files

CreateReadCountPanelOfNormals (GATK)

-panel of normals file created from the samples specified as "Control" at the start of the analysis
CallCopyRatioSegments (GATK)

-genome-wide seg file representing the windows assessed for CNVs