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The log2ratio bedGraph is a bedGraph file where the values represent the log2 ratio. It provides a view of how the copy number of a sample differs from a reference and can be extremely useful to troubleshoot false positives/negatives in CNV calls. In addition, log2ratio bedGraph can be useful to detect sequencing artifacts (GC bias, mapping issues), rvaluate coverage uniformity (dropout regions, overrepresented regions) or identify batch effects (technical noise across samples).
- Log2ratio bedGraph for your cases launched using Nostos secondary analysis can be downloaded from the case overview page for secondary analysis under "Download data" drop down menu:
- Log2ratio bedGraph can be loaded as a track in IGV desktop app allowing variant scientists to inspect copy number variations (CNVs), detect artifacts, and assess data quality in genomic regions:
