Copy Number Variation (CNV) analysis (GATK4)

Modified on Sat, 2 Sep, 2023 at 2:31 PM

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