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.
Report
-a chromosome-level browser for visualizing CNV calls
Output Files
CreateReadCountPanelOfNormals (GATK)
CreateReadCountPanelOfNormals/panel_of_normals.hdf5
-panel of normals file created from the samples specified as "Control" at the start of the analysis
CallCopyRatioSegments (GATK)
CallCopyRatioSegments/ModelSegments/<SAMPLE_NAME>.called.seg
-genome-wide seg file representing the windows assessed for CNVs